Bibliography, page 2

1. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
   NCBI E-utilities esearch over PubMed and GEO DataSets, run 2026-09-22 by Q98 through a wrapper that refuses any response with an empty querytranslation

   Oncofusion knowledge-graph project (Q98-elongator-smyd3) · NCBI E-utilities 2026
   used by ELP3 - the catalytic subunit, the only Elongator protein with a real acetyltransferase domain, and the one whose loss in mouse blood causes marrow failure and then p53-mutant leukaemia
2. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
   UniProtKB Q96EB1 (ELP4_HUMAN) - Elongator complex protein 4 (hELP4) (PAX6 neighbor gene protein)

   UniProt Consortium · UniProtKB 2026
   used by ELP4 (PAXNEB) - a required subunit of Elongator, the one partner of the seven with a genuine histone-acetyltransferase connection, and the one whose fusion supplies only its last 43 residues
3. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
   RefSeq NM_019040.4 - Homo sapiens elongator acetyltransferase complex subunit 4 (ELP4), mRNA

   NCBI RefSeq · NCBI Nucleotide 2026
   used by ELP4 (PAXNEB) - a required subunit of Elongator, the one partner of the seven with a genuine histone-acetyltransferase connection, and the one whose fusion supplies only its last 43 residues
4. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.dataset
   DepMap CRISPR (Chronos) gene-effect scan of 11 KMT2A-rearranged versus 43 other leukaemia lines (this project's own scan)

   Broad Institute DepMap; joined locally from analyses/depmap-kmt2a-selective-scan-full · analyses/depmap-kmt2a-selective-scan-full 2026
   used by ELP4 (PAXNEB) - a required subunit of Elongator, the one partner of the seven with a genuine histone-acetyltransferase connection, and the one whose fusion supplies only its last 43 residues
5. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
   UniProtKB Q8TE02 (ELP5_HUMAN) - reviewed human record, length 300 aa

   UniProt Consortium · UniProtKB 2026
   used by ELP5 (DERP6) - the bridge that joins ELP3 to ELP4, the most essential Elongator subunit in DepMap, and a gene whose cytoplasmic call rests on an overexpression experiment
6. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
   UniProtKB Q0PNE2 (ELP6_HUMAN) - reviewed human record, length 266 aa

   UniProt Consortium · UniProtKB 2026
   used by ELP6 (TMEM103/C3orf75) - an Elongator subunit named after a membrane protein it is not, whose entire localisation record comes from a Drosophila paper its own symbol cannot retrieve
7. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.trial_registry
   ClinicalTrials.gov API v2 query for intervention 'eltanexor'

   ClinicalTrials.gov · ClinicalTrials.gov 2026
   used by Eltanexor (KPT-8602) - the second-generation SINE whose whole point is that you can give it more often
8. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.reviewPMID 42071259
   Targeting the nuclear export receptor exportin-1 in acute myeloid leukaemia: From biology to clinical translation.

   Liu Y, Yun X, Ding W, et al. · Clinical and Translational Medicine 2026
   used by Eltanexor (KPT-8602) - the second-generation SINE whose whole point is that you can give it more often
9. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 41514668
   Characterizing KMT2A Rearrangement in Acute Myeloid Leukemia: A Comprehensive Genomic Study.

   Batayneh O, Moein M, Naji NS, et al. · Cancers (Basel) 2026
   used by Enasidenib - an approved mutant-IDH2 inhibitor sitting next to the one methylome co-mutation that IS enriched in KMT2A-rearranged AML, and never tested there, IDH and TET2 mutations are mutually exclusive in AML - so 'IDH2 enriched, TET2 depleted' in one cohort is ONE observation, not two, IDH1 - the same oncometabolite, the same assay, and NO enrichment in KMT2A-rearranged AML (6.7% vs 7.6%, p = 0.53): the control that makes the IDH2 result interpretable, IDH2 - the hypermethylating co-mutation that IS enriched in KMT2A-rearranged AML (16.0% vs 10.4%), at p = 0.0004 and not the p < 0.0001 the abstract claims, If the fusion's address requires unmethylated CpG, a hypermethylating co-mutation should be selected AGAINST - and IDH2 is selected FOR, which means the address is not the limiting resource, Is the CpG address a contested resource? On current evidence, no - and the beat that went looking says so, Ivosidenib - the approved IDH1 inhibitor, recorded here so that nobody reaches for it: IDH1 is the paralogue that is NOT enriched in KMT2A-rearranged AML, No IDH inhibitor has ever been reported in KMT2A-rearranged leukaemia: 4 literature records, all reviews, and 1 registry record, an adult master protocol - and the first version of this query returned a false zero, Put mutant IDH2 into SEM and ask three questions at once: does the unmethylated-CpG pool shrink, does the fusion move, and does its competitor move, TET2 is NOT a CXXC protein - its CXXC domain is a separate gene, and it is DEPLETED in KMT2A-rearranged AML rather than enriched, The methylome co-mutation table, recomputed: IDH2 up at p = 0.0004 and not p < 0.0001, IDH1 and DNMT3A flat, and the abstract disagrees with its own Table 2
10. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.trial_registry
    A Master Protocol for Biomarker-Based Treatment of AML (The Beat AML Trial)

    Beat AML, LLC · ClinicalTrials.gov 2026
    used by Enasidenib - an approved mutant-IDH2 inhibitor sitting next to the one methylome co-mutation that IS enriched in KMT2A-rearranged AML, and never tested there, Ivosidenib - the approved IDH1 inhibitor, recorded here so that nobody reaches for it: IDH1 is the paralogue that is NOT enriched in KMT2A-rearranged AML, No IDH inhibitor has ever been reported in KMT2A-rearranged leukaemia: 4 literature records, all reviews, and 1 registry record, an adult master protocol - and the first version of this query returned a false zero
11. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    ChEMBL molecule record CHEMBL3989908 (ENASIDENIB)

    ChEMBL, EMBL-EBI · ChEMBL database 2026
    used by Enasidenib - an approved mutant-IDH2 inhibitor sitting next to the one methylome co-mutation that IS enriched in KMT2A-rearranged AML, and never tested there
12. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    PubMed counted-absence search for KMT2A/MLL against ALDH2 and aldehyde dehydrogenase, run 2026-09-20 and title-checked

    · PubMed (NCBI) 2026
    used by Endogenous aldehydes and silenced ALDH2 — the rival explanation for an FA dependency in acute leukaemia, and the only one with an experiment behind it
13. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    GTEx v8 median gene expression (TPM) across 54 tissues, gtexportal.org API v2

    · GTEx Consortium / Broad Institute 2026
    used by ENL is the highest-expressed target in cerebellum and nobody has studied it there, Where else in the body each target is expressed, and the two controls that say the method works
14. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    PubMed E-utilities esearch, db=pubmed, run 2026-09-20 with querytranslation inspected

    NCBI Entrez Programming Utilities · NCBI E-utilities 2026
    used by ENL's disordered region and condensates, restricted to what actually bears on KMT2A::MLLT1 - which is one figure panel, Where KMT2A::MLLT1 actually sits: chromatin occupancy is mapped, subnuclear localisation of the endogenous fusion has never been imaged
15. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB Q03111 (ENL_HUMAN) - subcellular location comment with no evidence array, fetched 2026-09-20

    UniProt Consortium · UniProtKB 2026
    used by ENL's nuclear annotation has no citation at all, and every picture of ENL in a nucleus is of a mutant or a fusion, never the wild-type protein
16. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.analysis
    analyses/every-h2ak119ub-number-in-the-corpus/run.py and results.json, this repository; corpus read from git HEAD 2026-09-23; convention values from the committed results of q125-the-h2ak119ub-arm-of-the-pcgf1-knockout and q130-does-the-eviction-gradient-exist-in-h3k79me2

    Oncofusion knowledge graph, coordinator · internal analysis, reproducible from the repository 2026
    used by Enumerating every H2AK119ub number in 168 analysis result files instead of hand-picking fourteen: the two conventions flip sign on 35 of 68 comparable ratios but MATERIALLY on only 2, the exhaustive list finds exactly one real single-convention quotation against two arithmetic coincidences, and the statistic cycle 105 cited as proof they agree is one of the two places they materially disagree
17. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    Full-text retrieval test across eleven beat papers: Europe PMC core record for PMCID, then fullTextXML, then efetch db=pmc, testing for a body element

    Oncofusion knowledge graph, Q21 index-fusion-models beat · Europe PMC / NCBI eutils 2026
    used by Enumeration for the index-fusion model beat: what was searched, found, rejected and could not be read
18. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
    PubMed esearch, query: (KMT2A[tiab] OR MLL[tiab]) AND ("fusion partner"[tiab] OR "translocation partner"[tiab] OR "fusion partners"[tiab] OR "translocation partners"[tiab]) AND (prognosis[tiab] OR prognostic[tiab] OR outcome[tiab] OR outcomes[tiab] OR survival[tiab])

    National Center for Biotechnology Information · PubMed (NCBI E-utilities esearch) 2026
    used by Enumeration for the partner-outcome beat: what was searched, what was used, what was rejected, what could not be read
19. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
    PubMed E-utilities esearch, db=pubmed: eight subnuclear-compartment queries with query translations inspected, run 2026-09-20

    Not applicable - database query · NCBI E-utilities 2026
    used by Enumeration for the subnuclear beat: every compartment queried, every count, and the papers that looked on-topic and were not used
20. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    PubMed E-utilities esearch and efetch queries for USP2, USP8, MAML2, MAML3, SEPT3/SEPTIN3, SNX9 and menin intersections with MLL/KMT2A, run 2026-09-19

    National Center for Biotechnology Information (NCBI), PubMed · PubMed (NCBI E-utilities) 2026
    used by Enumeration for the USP2 / MAML2 / second-BCR beat: what was searched, what was counted, what was rejected, USP2 (ubiquitin carboxyl-terminal hydrolase 2) - the ninth commonest KMT2A partner and the only one that is a deubiquitinase
21. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
    PubMed E-utilities esearch and efetch, queries as stated, with querytranslation inspected and every returned title read

    National Library of Medicine · PubMed 2026
    used by Enumeration of candidate cooperating lesions in KMT2A-rearranged leukaemia - what was written, what was recorded as a gap, and what was read and rejected
22. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
    Europe PMC REST, four-route readability test run 2026-09-19

    Europe PMC · Europe PMC 2026
    used by Enumeration of the reciprocal KMT2A fusion literature: what was searched, found, rejected and could not be read
23. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
    Q22 phospho-contacts enumeration: kinase-substrate relations on KMT2A and its fusions, with retained/lost calls, bounded rejections and bounded unreadables

    · Oncofusion knowledge graph (internal enumeration) 2026
    used by Enumeration: every phosphorylation-dependent and kinase-regulated contact on KMT2A and its fusions that this beat could find
24. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    Oncofusion knowledge graph, interface-psip1-ibd-kmt2a: LEDGF IBD-KMT2A interface entry, read 2026-09-19

    · Oncofusion knowledge graph (internal) 2026
    used by Enumeration: every phosphorylation-dependent and kinase-regulated contact on KMT2A and its fusions that this beat could find
25. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB Q09472 (EP300_HUMAN), Histone acetyltransferase p300

    · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
    used by EP300 — the acetyltransferase whose paralogue split is the finding: p300 is the 108th most KMT2A-selective gene, CBP is the 16,950th
26. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
    PubMed E-utilities esearch record counts for EP300 and p300 against KMT2A, MLL and MLL-fusion terms, run for this beat

    · NCBI PubMed, queried 2026-09-19 2026
    used by EP300 — the acetyltransferase whose paralogue split is the finding: p300 is the 108th most KMT2A-selective gene, CBP is the 16,950th
27. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB entry Q09472 (EP300_HUMAN) feature table, retrieved live 2026-09-24 by q173 via an organism-restricted reviewed gene_exact search returning exactly one record

    · UniProt Consortium 2026
    used by EP300::ZNF384 - the commonest ZNF384 fusion, and it throws away the acetyltransferase
28. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
    UniProtKB Q96L91 (EP400_HUMAN), E1A-binding protein p400, 3159 aa

    · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
    used by EP400 - the ATPase that swaps H2A.Z in; its complex is required by MLL leukaemia stem cells, and in DepMap it is one of the three genes LEAST required in KMT2A-rearranged lines
29. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB Q96L91 (EP400_HUMAN), SUBCELLULAR LOCATION comment with its full evidence array and TISSUE SPECIFICITY, fetched live 2026-09-21

    UniProt Consortium · Databases 2026
    used by EP400 - the ATPase that swaps H2A.Z in; its complex is required by MLL leukaemia stem cells, and in DepMap it is one of the three genes LEAST required in KMT2A-rearranged lines
30. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB Q9Y2J2 (E41L3_HUMAN) function, subunit, subcellular-location evidence codes, tissue specificity and features; HGNC:3380 prev_symbol and alias_symbol via rest.genenames.org; retrieved 2026-09-22

    · UniProt Consortium / HGNC 2026
    used by EPB41L3 / DAL-1 - a membrane-skeleton tumour suppressor that binds and modulates two arginine methyltransferases, and whose own promoter methylation is a clinical test
31. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    NCBI E-utilities esearch, db=pubmed, querytranslation read back from every response, run 2026-09-22

    · NCBI PubMed 2026
    used by EPB41L3 / DAL-1 - a membrane-skeleton tumour suppressor that binds and modulates two arginine methyltransferases, and whose own promoter methylation is a clinical test
32. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    IntAct REST findInteractions/Q9Y2J2 (288 indexed interactions), filtered to Q03164/O00255/O75475/Q9UHB7/Q8TEK3/P51825/Q03111/P42568/P55199/P55197 with ac, experimentalRole, detectionMethod, hostOrganism and publicationPubmedIdentifier read per row; retrieved 2026-09-22

    · IntAct molecular interaction database (EMBL-EBI) 2026
    used by EPB41L3 / DAL-1 - a membrane-skeleton tumour suppressor that binds and modulates two arginine methyltransferases, and whose own promoter methylation is a clinical test
33. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
    analyses/depmap-kmt2a-selective-scan-full/results.json - 17,728 protein-coding genes, 11 Cellosaurus-annotated KMT2A-rearranged versus 43 other leukaemia lines, computed 2026-09-19

    · DepMap (Broad Institute), via this repository's scan 2026
    used by EPB41L3 / DAL-1 - a membrane-skeleton tumour suppressor that binds and modulates two arginine methyltransferases, and whose own promoter methylation is a clinical test
34. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    HGNC:19876 (EPC1, 'enhancer of polycomb 1') and UniProtKB Q9H2F5 (EPC1_HUMAN)

    · HGNC / UniProt 2026
    used by EPC1 - the NuA4/TIP60 subunit whose C-terminal fragment grips MBTD1, making it the contact a leukaemic fusion cannot do without and the mildest dependency in that whole complex
35. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    UniProtKB Q05BQ5 (MBTD1_HUMAN) canonical sequence, fetched as FASTA and indexed positionally; offset convention as derived and labelled in the graph entry fusion-zmynd11-mbtd1

    · UniProt 2026
    used by EPC1 - the NuA4/TIP60 subunit whose C-terminal fragment grips MBTD1, making it the contact a leukaemic fusion cannot do without and the mildest dependency in that whole complex
36. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB Q15375 - Ephrin type-A receptor 7 (Homo sapiens), reviewed

    UniProt Consortium · UniProtKB/Swiss-Prot 2026
    used by EPHA7 - ephrin type-A receptor 7, a published direct promoter target of the ALL1/AF4 (KMT2A::AFF1) fusion protein
37. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
    ana-q117-the-published-named-locus-pattern-reproduces-for-meis1-and-jmjd1c-and-breaks-for-mef2c-and-myb (this graph)

    Iqbal Lab oncofusion knowledge graph, beat Q117 · this project 2026
    used by EPHA7 is the one core member with a published KMT2A::AFF1 promoter ChIP - and this beat's own data put it second on separation while denying it to the AF9 samples
38. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB entry P42566 (EPS15_HUMAN), epidermal growth factor receptor substrate 15

    UniProt Consortium · UniProtKB 2026
    used by EPS15 / AF1p — domain architecture, and the one coordinate nobody has published
39. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    InterPro entry-to-protein matches for UniProt P42566

    InterPro / EMBL-EBI · InterPro 2026
    used by EPS15 / AF1p — domain architecture, and the one coordinate nobody has published
40. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 41265435
    Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukemia.

    Lewis AC, Gruber E, Franich R, Armstrong J, Kelly MJ, Opazo CM, et al., Kats LM · Cell 2026
    used by Erythroid progenitor - the committed red-cell precursor, distinct from the bipotent MEP that two entries had to borrow, and the compartment that pays for any haem-pathway or fetal-globin intervention, The OXPHOS-dependent state — established in KMT2A-rearranged AML, and inverted in KMT2A-rearranged B-ALL where OXPHOS inhibition makes leukaemia-initiating cells appear
41. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB P03372 (ESR1_HUMAN), Estrogen receptor

    · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
    used by ESR1 / estrogen receptor alpha - menin's best-documented non-leukaemic partner, and the only one a menin inhibitor is being given to patients to disrupt on purpose
42. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB P03372 (ESR1_HUMAN) SUBCELLULAR LOCATION comment, fetched 2026-09-21

    · UniProt Consortium 2026
    used by ESR1 / estrogen receptor alpha - menin's best-documented non-leukaemic partner, and the only one a menin inhibitor is being given to patients to disrupt on purpose
43. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
    Human Protein Atlas v25.1, subcellular (immunofluorescence) and Blood Atlas records for ESR1, fetched 2026-09-21

    · Human Protein Atlas 2026
    used by ESR1 / estrogen receptor alpha - menin's best-documented non-leukaemic partner, and the only one a menin inhibitor is being given to patients to disrupt on purpose
44. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    ENCSR000AHD - CTCF ChIP-seq in MCF-7; optimal IDR thresholded peaks ENCFF942TCG (GRCh38), default_analysis preferred_default

    Richard Myers, HudsonAlpha · ENCODE Portal 2026
    used by Estradiol does not redistribute SUV39H1 - because the replicates do not agree well enough to see it: over 56,171 CTCF anchors the ACROSS-condition Spearman (0.358) is HIGHER than the within-condition replicate correlations (0.326 for -E2, 0.207 for +E2), and the same 147 bp anchor reads 51.8, 69.1, 90.8 and 96.3 in the four samples, In MCF-7 the two signals point in opposite directions over the same 90 kb: H3K9me3 sits at the 15.8th and 10.3rd percentile of 56,171 same-cell CTCF anchors across the KMT2A gene body (0.82x and 0.65x the random-tile mean) while SUV39H1 sits at the 81.7th-86.8th in all four of its tracks - and the 147 bp anchor carries ZERO H3K9me3 in the minus-estradiol track, The MCF-7 arm, and the clause that saved it: SUV39H1 at the exon-11 anchor reaches the 96.3rd percentile of 56,171 same-cell-type CTCF anchors in one replicate - but all six non-anchor KMT2A intervals are elevated too (medians 73-87), so the pre-registered FIRES clause does not fire, the verdict is NEITHER, and four replicates of one antibody in one cell line span 51.8 to 96.3 at the same 147 bp, Two more independent cell types put the KMT2A exon-11 CTCF summit within 12 bp of the coordinate this graph carries: MCF-7 at chr11:118,488,689 (5 bp away) and SK-N-SH at chr11:118,488,682 (12 bp), both score-1000 optimal-IDR peaks - and in the same tracks the anchor ranks only 72.95th of 56,171 MCF-7 anchors, so it is an unambiguous anchor and an ordinary one
45. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    ChEMBL molecule and mechanism records: CHEMBL44657 (ETOPOSIDE) and CHEMBL1200645 (ETOPOSIDE PHOSPHATE); mechanism target CHEMBL2094255 'DNA topoisomerase II', target_type PROTEIN FAMILY

    · ChEMBL (EMBL-EBI) 2026
    used by Etoposide (VP-16) - the drug that makes this disease and cures several others, and the only entry in this graph whose main finding is that you must not stop using it, TOP2B - the isoform most etoposide-induced KMT2A breaks depend on, resolved genetically and not resolvable pharmacologically
46. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB entry P41212 (ETV6_HUMAN): reviewed sequence, length and positional feature annotations

    UniProt Consortium · UniProtKB/Swiss-Prot 2026
    used by ETV6 — domain architecture and residue coordinates
47. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    AlphaFold Protein Structure Database entry for P41212 (model AF-P41212-F1)

    Jumper J, Varadi M, et al.; EMBL-EBI/DeepMind · AlphaFold DB 2026
    used by ETV6 — domain architecture and residue coordinates
48. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    InterPro member-database domain matches for UniProt P41212 (Pfam, PROSITE, SMART, CDD, CATH-Gene3D, SUPERFAMILY)

    InterPro Consortium; EMBL-EBI · InterPro 2026
    used by ETV6 — domain architecture and residue coordinates
49. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    SIFTS UniProt residue-level mappings for PDB entries 2DAO, 1JI7, 1LKY, 5L0P (construct ranges read back from the PDBe mappings API)

    PDBe / SIFTS; EMBL-EBI · PDBe SIFTS 2026
    used by ETV6 — domain architecture and residue coordinates
50. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.analysis
    Literature recall of the Oncofusion knowledge graph against five stated PubMed queries, and the laboratories it never cites

    · Oncofusion knowledge graph (internal analysis) 2026
    used by Every age-restricted target nominated by the model is pan-essential or invisible, IGF2BP3 — an RNA-binding protein required for MLL-Af4 leukaemogenesis in mice that CRISPR barely touches in human lines, The 3.7% was mostly the query: DOT1L recall is 19.6% once you ask about leukaemia, We have read a tenth of the recent field, and the gap found a real interactor
51. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    DepMap CRISPR (Chronos) gene effect retrieved through the Open Targets Platform GraphQL API, as persisted across the Oncofusion knowledge graph's DepMap analyses

    · DepMap / Open Targets Platform 2026
    used by Every DOT1L dependency number this project has computed, in one place, lineage-split and in raw Chronos units
52. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
    Lineage confound in myeloid transcription-factor dependencies: splitting the KMT2A-rearranged arm (Oncofusion KG analysis)

    · Oncofusion knowledge graph (internal analysis) 2026
    used by Every DOT1L dependency number this project has computed, in one place, lineage-split and in raw Chronos units
53. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.analysis
    Is the lineage-consistency ranking a ranking of effect size or of narrowness? (Oncofusion KG analysis)

    · Oncofusion knowledge graph (internal analysis) 2026
    used by Every DOT1L dependency number this project has computed, in one place, lineage-split and in raw Chronos units
54. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
    Power of the DepMap panel to detect a MEN1-scale dependency in rearranged arms (Oncofusion KG analysis)

    · Oncofusion knowledge graph (internal analysis) 2026
    used by Every DOT1L dependency number this project has computed, in one place, lineage-split and in raw Chronos units
55. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
    Does the MEN1 co-dependency signal survive lineage adjustment? (Oncofusion KG analysis)

    · Oncofusion knowledge graph (internal analysis) 2026
    used by Every DOT1L dependency number this project has computed, in one place, lineage-split and in raw Chronos units
56. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    Cellosaurus: search for KMT2A-MLLT1 and individual accession records CVCL_1866, CVCL_8227, CVCL_8485, CVCL_3991, CVCL_6865, CVCL_3937, CVCL_W777

    Bairoch A, et al.; Cellosaurus · Cellosaurus (SIB) 2026
    used by Every human t(11;19) KMT2A::MLLT1 cell line, with accessions fetched and read back - and not one of them is known to be reciprocal-negative
57. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    Cellosaurus cell line records fetched by accession

    · Cellosaurus (SIB) 2026
    used by Every human t(9;11) cell line, with every accession fetched and read back: eleven lines, ten patients, and two of them are B-ALL, THP-1 (CVCL_0006): the default KMT2A::MLLT3 line, from a one-year-old, carrying NRAS G12D and a TP53 frameshift
58. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset
    ana-kmt2a-exon-to-domain-map (this graph) - Ensembl ENST00000534358 CDS exon boundaries intersected with UniProt Q03164

    · this project; Ensembl REST; UniProt REST 2026
    used by Every MS-evidenced KMT2A modification site, flagged retained or lost against the breakpoint - and the retained portion is NOT enriched for acetylation once you use the right null, Which KMT2A exon carries which interface: exon 1 is the menin-binding motif, exons 5-6 are the CXXC zinc finger (computed, not recalled)
59. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset
    analyses/q165-the-retained-acetylation-site/retained-enrichment-null.py

    · this project 2026
    used by Every MS-evidenced KMT2A modification site, flagged retained or lost against the breakpoint - and the retained portion is NOT enriched for acetylation once you use the right null, KMT2A K1130 acetylation - the clock-controlled, SIRT1-erased site that every KMT2A fusion retains, 17 residues from the CXXC and 208 from the breakpoint, KMT2A K1130 ubiquitination - the same retained lysine as the clock acetylation site, carrying a chemically exclusive second mark that no KMT2A paper has ever mentioned, KMT2A K1133 acetylation - the better-evidenced half of the pair, and the one that appears in the CBP/p300 acetylome itself, KMT2A K636 acetylation - the forgotten member of the Choudhary quartet, retained, and outside the SIRT1-interaction region, Ranked against four fusion families, the KMT2A acetylation site is the only candidate with no evidence on the fusion at all - and the strongest argument for it is one nobody has made, Resolve acetyl-K1130/K1133 occupancy on the fusion versus wild-type KMT2A in the same cell - the one experiment that makes a shared-sequence site interpretable, The K1130/K1133 numbering is HUMAN, stated in the paper's own words, and the immunising peptide proves it a second time without relying on that sentence, What was searched for a structure and what came back empty: the KMT2A interface layer enumerated by accession pair, with the graph's own unmapped interfaces listed
60. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB Q03164 (KMT2A_HUMAN) feature table - MOD_RES, CROSSLNK, SITE, CHAIN

    · UniProt 2026
    used by Every MS-evidenced KMT2A modification site, flagged retained or lost against the breakpoint - and the retained portion is NOT enriched for acetylation once you use the right null, KMT2A K1235 acetylation - inside the SIRT1-interaction region, retained, and the one member of the Choudhary quartet the source paper named and then never assayed, KMT2A K1364 SUMO - the one modification site inside the breakpoint cluster, retained in some patients' fusion proteins and lost in others, KMT2A K2528 SUMO2 - the single best-supported modification site on the whole protein, in the N320 fragment, and LOST in every fusion, The partner, not the site, is what could make a retained KMT2A modification fusion-specific - the AML1-ETO mechanism asked of KMT2A::AFF1
61. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
    check-dangling-data-refs.py output re-analysed by author-cycle provenance and by fuzzy match against the live id set

    · Oncofusion knowledge graph (internal) 2026
    used by Every multi-entry dangling reference in this graph has exactly one author: demand counts entries, and entries are not independent, Seventeen entries declare themselves part of a causal chain that does not exist, and the validator could not see it
62. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
    PubMed esearch, two stated queries run 2026-09-20: ('MLL-AF4'[tiab] OR 'MLL::AF4'[tiab] OR 'KMT2A::AFF1'[tiab] OR 'KMT2A-AFF1'[tiab]) AND (knock-in[tiab] OR knockin[tiab] OR degron[tiab] OR dTAG[tiab] OR 'endogenously tagged'[tiab]) returns 1 (PMID 16551973, a murine fusion-gene knock-in, not a tag knock-in); (KMT2A[tiab] OR MLL[tiab]) AND ('endogenously tagged'[tiab] OR 'endogenous tagging'[tiab] OR dTAG[tiab]) returns 0

    · NCBI E-utilities 2026
    used by Every published MLL-fusion degron tags an overexpressed construct, not the endogenous allele - and that distinction decides what the washout kinetics mean, The experiment nobody has done: an epitope tag knocked into the endogenous KMT2A fusion allele in a patient-derived line
63. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB REST search API, gene_exact queries with fields=accession,id,gene_primary,gene_synonym,protein_name,length, run 2026-09-20

    UniProt Consortium · UniProt 2026
    used by Every upstream NF-kB component this beat enumerated, with its query, its count, and why it did or did not get an entry
64. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    PubMed E-utilities esearch and esummary, db=pubmed, run 2026-09-20

    NCBI · PubMed 2026
    used by Every upstream NF-kB component this beat enumerated, with its query, its count, and why it did or did not get an entry
65. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB entry Q01844 (EWS_HUMAN): reviewed sequence, length and positional feature annotations

    UniProt Consortium · UniProtKB/Swiss-Prot 2026
    used by EWSR1 — domain architecture and residue coordinates, EWSR1::ZNF384 - the same EWSR1 exon 7 fragment that drives Ewing sarcoma, fused instead to a zinc-finger protein, in B-ALL, EWSR1::ZNF384 versus EWSR1::FLI1 - the same EWSR1 exon-7 module on two different DNA-binding proteins, and nobody has compared them
66. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    InterPro/Pfam/CATH-Gene3D/SUPERFAMILY domain matches for UniProt Q01844

    InterPro Consortium; EMBL-EBI · InterPro 2026
    used by EWSR1 — domain architecture and residue coordinates
67. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    Ensembl transcript ENST00000397938 (EWSR1): exon structure and coding-sequence coordinates, used to convert exon breakpoints into residue numbers

    Ensembl; EMBL-EBI · Ensembl REST API 2026
    used by EWSR1 — domain architecture and residue coordinates
68. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    AlphaFold Protein Structure Database entry for Q01844 (model AF-Q01844-F1)

    Jumper J, Varadi M, et al.; EMBL-EBI/DeepMind · AlphaFold DB 2026
    used by EWSR1 — domain architecture and residue coordinates
69. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB Q01844 (EWS_HUMAN) and Q01543 (FLI1_HUMAN) feature tables

    · UniProt 2026
    used by EWSR1::FLI1 has no residue-resolved, fusion-demonstrated PTM in its retained portion - every mapped site falls past the breakpoint, and the one site shown on the fusion has no residue
70. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB Q9UQ84 (EXO1_HUMAN) - Exonuclease 1, Homo sapiens

    UniProt Consortium · UniProt Knowledgebase 2026
    used by EXO1 (Q9UQ84, 846 aa) - the long-range resection nuclease at the bottom of the CTCF cascade, and the point where this graph's two independent 2026 HR papers meet: CtIP starts the resection, EXO1/DNA2 finish it
71. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    NCBI E-utilities esearch over PubMed, db=pubmed, retmode=json, querytranslation read back for every query

    National Center for Biotechnology Information · NCBI Entrez Programming Utilities 2026
    used by EXO1 (Q9UQ84, 846 aa) - the long-range resection nuclease at the bottom of the CTCF cascade, and the point where this graph's two independent 2026 HR papers meet: CtIP starts the resection, EXO1/DNA2 finish it
72. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    ENCODE Portal experiment search, type=Experiment, assay_title=TF ChIP-seq, status=released, target.label=EXO1

    ENCODE Project Consortium · ENCODE Portal 2026
    used by EXO1 (Q9UQ84, 846 aa) - the long-range resection nuclease at the bottom of the CTCF cascade, and the point where this graph's two independent 2026 HR papers meet: CtIP starts the resection, EXO1/DNA2 finish it
73. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB Q13015 (AF1Q_HUMAN) Protein AF1q, Homo sapiens, 90 aa

    UniProt Consortium · UniProtKB 2026
    used by Experiment: does AF1q self-associate, and does KMT2A::MLLT11 transform? The two measurements nobody has made on the 10th most common KMT2A fusion, KMT2A::MLLT11 (MLL-AF1q), t(1;11)(q21;q23) — 28 patients, and not one functional experiment, MLLT11 / AF1q — a 90-residue protein with no chromatin domain and no oligomerisation module, KMT2A partner in t(1;11)(q21;q23)
74. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    PubMed eutils esearch, controlled intersection: menin-inhibitor half (216 records) x niche/stroma half (543,067 records) = 9 records, all titles read, none testing niche protection against a menin inhibitor

    NCBI E-utilities · NCBI Entrez 2026
    used by Experiment: does marrow stroma protect KMT2A-rearranged cells from a menin inhibitor? Nobody has run the week-long experiment that would say
75. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 41980221
    3D Chromosome Remodeling in B-cell Development and Acute Lymphoblastic Leukemia

    Ghebrechristos YE, Evensen NA, Cathelin RS, et al. · Blood cancer discovery 2026
    used by Experiment: measure KMT2A-AFF1 spatial proximity in the human fetal progenitor, in the cell and at the time the translocation actually happens
76. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB entry Q03164 (KMT2A_HUMAN) - canonical sequence, retrieved via the UniProt REST API and scanned for the HBM consensus

    UniProt Consortium; scan performed for this beat · UniProtKB 2026
    used by Experiment: put four residues back - the minimal add-back control the PHD3 result has never had, Ledger: every module the KMT2A half loses, with coordinates, how each was confirmed, and whether its loss has been shown to matter, Lost from the KMT2A half: both taspase1 cleavage sites (D2666 and D2718) - the fusion is never processed, Lost from the KMT2A half: PHD2 (aa 1479-1533), an E3 ubiquitin ligase that limits KMT2A's own activity, Lost from the KMT2A half: PHD3 and the bromodomain are one cassette, not two modules (aa 1566-1765), Lost from the KMT2A half: the four-residue HCF-binding motif (DHNY, aa 1799-1802), Lost from the KMT2A half: the FYRN-FYRC clamp (2018-2074 / 3666-3747) that holds wild-type KMT2A together, Lost from the KMT2A half: the SET domain (aa 3829-3945) - the lost module whose loss demonstrably does not matter, Lost from the KMT2A half: the transactivation domain (aa 2829-2883) and its CBP contact, Lost from the KMT2A half: the WIN motif and the whole WRAD interface (aa 3762-3767, Arg3765), The KMT2A N-terminal antibody reports wild-type plus fusion and the C-terminal antibody reports wild-type alone - which makes an N-versus-C difference a fusion-specific readout with no tag and no engineering, The menin that matters in an infant KMT2A-rearranged leukaemia is the menin on the fusion, and the N-minus-C antibody difference can measure it in any patient sample without a tag
77. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
    Negative PubMed search conducted for this graph on 2026-09-19 via the PubMed E-utilities: HCFC1 AND MLL AND leukemia; HCF-1 AND MLL AND transformation AND Hox. Only PMID 15199122 (Yokoyama 2004) and PMID 27009953 (an EBV OriP study) were returned among MLL-relevant hits

    Q-subtraction-kmt2a-counter · NCBI PubMed E-utilities 2026
    used by Experiment: put four residues back - the minimal add-back control the PHD3 result has never had
78. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    PubMed E-utilities esearch, counted-absence query for XPO1 inhibition and H3K79

    Oncofusion Knowledge Graph project (Q61-export-axis) · NCBI E-utilities 2026
    used by Export or docking? A locus-resolved H3K79me2 ChIP under an XPO1 inhibitor separates the two CALM-AF10 models, and it has never been run, Three measurements the export axis needs and nobody has published: XPO1 occupancy in KMT2A-r, H3K79 under an XPO1 inhibitor, and CRM1 occupancy under a menin inhibitor
79. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 42227701
    Ziftomenib with venetoclax and azacitidine in relapsed/refractory NPM1-mutated acute myeloid leukemia

    Wang ES, ... Issa GC · Blood 2026
    used by Eytan Stein (MSKCC), Ghayas Issa (MD Anderson) and the clinical menin-inhibitor investigator network
80. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.trial_registry
    ClinicalTrials.gov investigator and site records for menin-inhibitor trials in KMT2A-rearranged acute leukaemia, retrieved via the ClinicalTrials.gov API v2

    US National Library of Medicine · ClinicalTrials.gov 2026
    used by Eytan Stein (MSKCC), Ghayas Issa (MD Anderson) and the clinical menin-inhibitor investigator network
81. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB reviewed human record Q92800 (EZH1_HUMAN), resolved with gene_primary and length requested in fields

    · UniProt 2026
    used by EZH1 - the paralogue that makes the approved EZH2 drug the wrong drug for this disease
82. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 41438598
    Targeting dysregulated epigenetic and transcription factor networks in KMT2A-rearranged AML using iPSC models.

    Palau A; Thier J; Naughton A; Tae-Jun Kwon A; Cabrerizo Granados D; Hofmann S; Kaczkowski B; Zhong X; Lehmann S; Arner E; Lundin V; Lennartsson A · Blood Neoplasia 2026
    used by EZH1 - the paralogue that makes the approved EZH2 drug the wrong drug for this disease
83. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB reviewed human record Q15910 (EZH2_HUMAN), resolved with gene_primary and length requested in fields

    · UniProt 2026
    used by EZH2 - the Polycomb enzyme that collaborates with the fusion instead of opposing it, and that no single-agent inhibitor can switch off
84. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    HGNC:33738 (EZHIP, 'EZH inhibitory protein') and UniProtKB Q86X51 (EZHIP_HUMAN)

    · HGNC / UniProt 2026
    used by EZHIP (CXorf67, CATACOMB) - a protein that jams PRC2 by pretending to be an H3K27M oncohistone, and the 3' payload of MBTD1's other fusion, MBTD1 is the effector-recruiting half of a leukaemia fusion and the addressing half of a sarcoma fusion while donating nearly all of itself to both - so the junction, not the parts, assigns the role
85. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.reviewPMID 42238311
    CXorf67 in malignancies: Deciphering epigenetic landscapes and clinical implications for precision oncology.

    Yu X, Wu H, Lan Y, Chen W, Liu J · Genes Dis 2026
    used by EZHIP (CXorf67, CATACOMB) - a protein that jams PRC2 by pretending to be an H3K27M oncohistone, and the 3' payload of MBTD1's other fusion, Low-grade endometrial stromal sarcoma is a family of NuA4-acetyltransferase-to-Polycomb fusions, and that is why one of MBTD1's two fusions looks nothing like the other, MBTD1::EZHIP (MBTD1-CXorf67), t(X;17)(p11.2;q21.33) - MBTD1's other fusion, in which a NuA4 subunit delivers an H3K27M-mimicking PRC2 poison to low-grade endometrial stromal sarcoma
86. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    scripts/is-symbol-covered.py run over 2,340 node files (HGNC rows 45,083, retired/alias index 58,536) and NCBI esearch db=pubmed via scripts/pubmed_safe.py, both 2026-09-23. querytranslations read back from each response, e.g. "EZHIP"[Title/Abstract] AND "H3K27me3"[Title/Abstract]. Counts and id lists persisted to analyses/q123-the-architecture-from-other-parts-analogy/bounded-searches.json

    · oncofusion-knowledge-graph tooling and NCBI PubMed 2026
    used by EZHIP (CXorf67, CATACOMB) - a protein that jams PRC2 by pretending to be an H3K27M oncohistone, and the 3' payload of MBTD1's other fusion
87. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB entry Q0VG06

    · UniProtKB/Swiss-Prot 2026
    used by FAAP100 — FA core complex; rank 36 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all
88. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    PubMed counted absence search for FAAP100 against KMT2A/MLL, run 2026-09-20 with aliases and title-checked

    · PubMed (NCBI) 2026
    used by FAAP100 — FA core complex; rank 36 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all
89. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
    PubMed E-utilities esearch record counts for the FACT complex and its subunits against KMT2A, MLL, the super elongation complex and DOT1L, run for interactome round 5

    · NCBI PubMed, queried 2026-09-19 2026
    used by FACT (SPT16-SSRP1) - the chromatin arm of transcription elongation, and a clean negative result for the KMT2A::AFF1 interactome
90. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
    openFDA drug/event API query of FAERS for menin-inhibitor endocrine and bone-mineral adverse event terms

    US Food and Drug Administration (data); analysis run for this graph, analyses/faers-menin-inhibitor-endocrine/run.py · openFDA FAERS, queried 2026-09-18 2026
    used by FAERS shows no endocrine signal for either menin inhibitor - and proves it could not have, Hypothesis: the PTH rise on menin inhibitors is on-target and exposure-dependent, not renal
91. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB entry O15360

    · UniProtKB/Swiss-Prot 2026
    used by FANCA — FA core complex; rank 20 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all
92. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    PubMed counted absence search for FANCA against KMT2A/MLL, run 2026-09-20 with aliases and title-checked

    · PubMed (NCBI) 2026
    used by FANCA — FA core complex; rank 20 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all, FANCG — FA core complex; rank 27 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all
93. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
    PubMed E-utilities esearch, 2026-09-21. the 78-record foci/chromatin count was NOT title-checked and is quoted as a literature size, not as a count of on-topic papers

    · NCBI PubMed 2026
    used by FANCA — FA core complex; rank 20 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all
94. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB entry Q9BXW9 (FANCD2_HUMAN, Fanconi anemia group D2 protein)

    · UniProtKB/Swiss-Prot 2026
    used by FANCD2 — the FA effector menin binds, and the weakest FA gene in this graph's own selectivity scan
95. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    PubMed counted-absence search for FANCD2 against KMT2A/MLL, run 2026-09-20, aliases searched and every hit title-checked

    · PubMed (NCBI) 2026
    used by FANCD2 — the FA effector menin binds, and the weakest FA gene in this graph's own selectivity scan
96. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB entry Q9NPI8

    · UniProtKB/Swiss-Prot 2026
    used by FANCF — FA core complex; rank 11 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all
97. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
    PubMed counted absence search for FANCF against KMT2A/MLL, run 2026-09-20 with aliases and title-checked

    · PubMed (NCBI) 2026
    used by FANCF — FA core complex; rank 11 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all
98. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB entry O15287

    · UniProtKB/Swiss-Prot 2026
    used by FANCG — FA core complex; rank 27 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all
99. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
    UniProtKB entry Q9NVI1

    · UniProtKB/Swiss-Prot 2026
    used by FANCI — ID2 module; rank 15 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all, The FA core complex does not move together, and that is the strongest argument against reading this as a Fanconi-pathway dependency at all
100. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted absence search for FANCI against KMT2A/MLL, run 2026-09-20 with aliases and title-checked

     · PubMed (NCBI) 2026
     used by FANCI — ID2 module; rank 15 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all
101. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q9NW38

     · UniProtKB/Swiss-Prot 2026
     used by FANCL — FA core complex; rank 26 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all
102. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted absence search for FANCL against KMT2A/MLL, run 2026-09-20 with aliases and title-checked

     · PubMed (NCBI) 2026
     used by FANCL — FA core complex; rank 26 of 8,269 for KMT2A-selective dependency, and no KMT2A literature at all
103. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q6PCT2 (FXL19_HUMAN), F-box/LRR-repeat protein 19

     UniProt Consortium · UniProtKB 2026
     used by FBXL19 - a CpG-island reader that delivers CDK-Mediator and RNF20 to developmental promoters, and whose experimental localisation is mostly cytoplasm
104. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     Cell Ontology search for pro-B and pre-pro-B terms via the EMBL-EBI Ontology Lookup Service OLS4 API

     EMBL-EBI Ontology Lookup Service; Cell Ontology consortium · Database 2026
     used by Fetal CD19+CD34+CD10-negative PreProB progenitor — a cell that exists before birth and almost not at all after
105. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Cell Ontology (CL) term lookup via the EMBL-EBI Ontology Lookup Service OLS4 API

     EMBL-EBI Ontology Lookup Service; Cell Ontology consortium · Database 2026
     used by Fetal liver haematopoietic stem and progenitor cell — the leading candidate cell of origin for t(4;11) infant ALL
106. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 42213620
     The fetal specific gene LIN28B is essential for human fetal B-lymphopoiesis and initiation of KMT2A::AFF1 infant leukemia.

     Ling RE, Welsh AM, Hamer L, Jackson T, Neil E, Elliott N, et al. · Blood 2026
     used by Fetal-restricted permissive factors across fusion families - the class has exactly ONE fully worked member, and for ETV6::RUNX1 the fetal advantage is real but no factor is named, LIN28B - a one-row BioID prey of KMT2A that a 2026 Blood paper shows is REQUIRED for KMT2A::AFF1 to transform human fetal cells, LIN28B has THREE published signs in myeloid leukaemia - oncogene, tumour suppressor, and differentiation agent - and the design quality runs opposite to the direction the index-fusion story needs, LIN28B has two routes - blocking let-7, and binding mRNAs directly - and in KMT2A::AFF1 every published mechanism is the direct-mRNA one (let-7 IS measured in mouse MLL-fusion AML: in-session correction), LIN28B-dependent fetal B- and NK-lymphopoiesis - the NORMAL state the leukaemia requirement is parasitic on, and the reason the therapeutic window is narrow by construction, PROPOSED: measure let-7 and restore it in the human fetal-liver KMT2A::AFF1 model - an axis measured in mouse MLL-fusion AML but never in the index fusion, PROPOSED: run a second oncogene in LIN28B-null human fetal liver CD34+ cells - the control that decides whether the KMT2A::AFF1 transformation block is fusion-specific or just a broken progenitor, PROPOSED: swap the partner, hold everything else - KMT2A::MLLT3 versus KMT2A::AFF1 in LIN28B-null human fetal liver CD34+ cells, PUBLISHED, DONE: human fetal liver CD34+ cells fail to transform on KMT2A::AFF1 induction without LIN28B (Ling et al., Blood 2026) - a dedicated human index-fusion experiment, read from the abstract only, Reading the same-source counter-evidence: 77 notes adjudicated, and the defect is not the one the metric measures, Retained fetal programme — the infant-versus-adult stem cell difference, and the reason KMT2A::AFF1 needs no second mutation, Targeting LIN28B - the essential-function and wrong-sign risks are established by the SAME paper that makes it interesting, and the sign may reverse with lineage, The fetal state is PERMISSIVE for lymphoid KMT2A-fusion transformation and PROTECTIVE against myeloid - which is why LIN28B has opposite signs in the two literatures, Two groups invoke LIN28B to explain the SAME epidemiological fact in OPPOSITE directions - and neither claim is the one this graph has been repeating
107. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI E-utilities esearch against PubMed, run via scripts/pubmed_safe.py with querytranslation recorded for every query

     2026
     used by Fetal-restricted permissive factors across fusion families - the class has exactly ONE fully worked member, and for ETV6::RUNX1 the fetal advantage is real but no factor is named
108. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42643519
     Successful treatment of relapsed KMT2A-rearranged AML with central nervous system involvement using revumenib in combination with venetoclax and azacitidine: A case report

     Xu J, Chen Y, Zhang Y, Zhang F, Zhang Y, Sun J, Xu N · Therapeutic Advances in Hematology 2026
     used by Fever and headache thirty-two months after transplant: KMT2A::AFDN AML relapsing into the CNS, and a menin inhibitor that cleared the spinal fluid, Menin dependence of a non-elongation KMT2A fusion has never been demonstrated — the counted absence, and what the pivotal trial actually enrolled
109. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.trial_registry
     FHD-286 as Monotherapy or Combination Therapy in Subjects With Advanced Hematologic Malignancies

     ClinicalTrials.gov, raw API v2 read 2026-09-20 · ClinicalTrials.gov 2026
     used by FHD-286 - the dual BRG1/BRM inhibitor that carries every SWI/SNF therapeutic claim in this disease, with a minimum enrolment age of 16
110. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.trial_registry
     FHD-286 in Subjects With Metastatic Uveal Melanoma

     ClinicalTrials.gov, raw API v2 read 2026-09-20 · ClinicalTrials.gov 2026
     used by FHD-286 - the dual BRG1/BRM inhibitor that carries every SWI/SNF therapeutic claim in this disease, with a minimum enrolment age of 16
111. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.trial_registry
     FHD-286 With Low-Dose Weekly Decitabine/Venetoclax in Patients With Acute Myeloid Leukemia

     ClinicalTrials.gov, raw API v2 read 2026-09-20 · ClinicalTrials.gov 2026
     used by FHD-286 - the dual BRG1/BRM inhibitor that carries every SWI/SNF therapeutic claim in this disease, with a minimum enrolment age of 16
112. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Cellosaurus CVCL_2119 (MOLM-13): Sequence variation - Gene fusion KMT2A + MLLT3 (MLL-AF9); FLT3-ITD heterozygous

     · Cellosaurus (SIB) 2026
     used by First deposit to put both drug classes on the MEN1 channel in one experiment: VTP-50469 leaves ZERO of the 19 DMSO menin peaks at 15 canonical menin-MLL target loci, while EPZ5676 keeps 14, compound 10 keeps 14 and compound 11 keeps 8 - strength-matched permutation p = 0.0003, and the zero is unchanged at every flank from 0 to 100 kb, In the same deposit, the MENIN inhibitor removes DOT1L from all five DMSO DOT1L peaks at canonical target loci (p = 0.0432) while all three DOT1L inhibitors keep 5/5 - and the VTP DOT1L library still calls ACTB, GAPDH and EEF1A1, which is the internal positive control the MEN1 arm lacks
113. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     Negative PubMed search: (BioID OR TurboID OR "proximity labeling") AND (KMT2A OR MLL) AND leukemia; and a second query adding interactome and proteomics terms. Both returned 0 results. Conducted for this graph on 2026-09-18 via the NCBI PubMed E-utilities

     Oncofusion Knowledge Graph project, using the NCBI PubMed E-utilities · Literature search 2026
     used by First systematic enumeration of the KMT2A fusion interactome, and the diff against this graph, Menin is the best handle on KMT2A::AFF1 because of where the break falls, not because menin is biologically special
114. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q01543 (FLI1_HUMAN): reviewed sequence, length and positional feature annotations

     UniProt Consortium · UniProtKB/Swiss-Prot 2026
     used by FLI1 — domain architecture and residue coordinates
115. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     PDB 1FLI 'DNA-BINDING DOMAIN OF FLI-1', 5E8G 'Crystal structure of the DNA binding domain of human transcription factor FLI1' and 6VGD 'Crystal structure of the DNA binding domain (DBD) of human FLI1 and the complex of the DBD of human Runx2 with core binding factor beta (Cbfb), in complex with 16mer DNA' (all titles retrieved and verified at RCSB)

     RCSB Protein Data Bank (entry metadata retrieved and title verified) · RCSB PDB 2026
     used by FLI1 — domain architecture and residue coordinates
116. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     Ensembl transcript ENST00000527786 (FLI1): exon structure and coding-sequence coordinates, used to convert exon breakpoints into residue numbers

     Ensembl; EMBL-EBI · Ensembl REST API 2026
     used by FLI1 — domain architecture and residue coordinates
117. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     AlphaFold Protein Structure Database entry for Q01543 (model AF-Q01543-F1)

     Jumper J, Varadi M, et al.; EMBL-EBI/DeepMind · AlphaFold DB 2026
     used by FLI1 — domain architecture and residue coordinates
118. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     RCSB PDB entries 1RJB, 4XUF, 6JQR and 7ZV9, each verified against the RCSB data API for title, experimental method and resolution

     RCSB Protein Data Bank · RCSB PDB 2026
     used by FLT3 / CD135 — the strongest non-tether co-dependency, and a target the field may have written off on a badly executed trial
119. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P36888 (FLT3_HUMAN), receptor-type tyrosine-protein kinase FLT3, retrieved via the UniProt REST API

     UniProt Consortium · UniProtKB 2026
     used by FLT3 / CD135 — the strongest non-tether co-dependency, and a target the field may have written off on a badly executed trial
120. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     cBioPortal for Cancer Genomics, study all_stjude_2015 (Acute Lymphoblastic Leukemia, St Jude, Nat Genet 2015) — FLT3 mutation records retrieved via the public REST API on 2026-09-18

     cBioPortal for Cancer Genomics · Database 2026
     used by FLT3 in KMT2A-r leukemia — near-universal overexpression, but activating mutation in only ~3% of infants, KRAS as a co-mutation in KMT2A-r leukemia — the single most frequently co-mutated gene, and it still cannot start the disease, NF1 in KMT2A-r leukemia — one homozygous deletion, one missense, and the only loss-of-function co-lesion in the disease, NRAS as a co-mutation in KMT2A-r leukemia — the one co-lesion that is specifically enriched in t(4;11), PTPN11 in KMT2A-r leukemia — named in every gene list, supported by almost no cases, The near-silent genome of infant KMT2A-r ALL — 1.3 non-silent mutations, and why that is bad news as well as good
121. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42566532
     MBNL1 hijacks a structured single-stranded distal DNA element to sustain FLT3 expression in KMT2A-rearranged leukemias.

     Che M, Fields S, et al. · Science advances 2026
     used by FLT3 is the second largest KMT2A-selective dependency and it is HEAVIER in B-lineage than in myeloid cells
122. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P36888 (FLT3_HUMAN) - subcellular location, fetched 2026-09-20

     UniProt Consortium · UniProtKB 2026
     used by FLT3-ITD signals from inside the cell, not from the surface - and whether it is the ER or the Golgi decides which pathway fires
123. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 41709524
     Physiologically Based Pharmacokinetic Virtual Twin Approach for Fludarabine Dosing in Pediatric Hematopoietic Stem Cell Transplantation.

     Mseddi M, Nath C, Ben Hassine K, Mlakar V, Gloor Y, Gonzales F, Uppugunduri CRS, Daali Y, et al. · CPT: Pharmacometrics & Systems Pharmacology 2026
     used by Fludarabine - the immunosuppressive half of modern conditioning, given as a phosphate prodrug, cleared by the kidney, and dosed by a body-surface-area rule that measurably fails in children, Infants are not small children - four maturing organ systems, three conditioning drugs, and a protocol that treats the first year of life as one category, The fludarabine prodrug chain - three molecules called by one name, and the one that is measured is neither the one given nor the one that works
124. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     HGNC complete set, protein-coding symbols and approved names, used to separate real gene symbols from the uppercase acronyms of a biology corpus

     · HUGO Gene Nomenclature Committee 2026
     used by Four beats in a row were picked by noticing the same shape by hand; this is the instrument that finds it - 171 gene symbols named in six or more entries with no entry of their own
125. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.analysis
     counted-absence-index-recheck: four recorded absences re-run against a second index with positive controls

     · Oncofusion knowledge graph (internal analysis) 2026
     used by Four counted absences re-run against a second index, and all four hold
126. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paperPMID 42131930
     Decoding WDR5-Mediated Interactions in Gliomas: Implications for Targeted Therapy

     Jung E, Piperi C · Medicinal Research Reviews 2026
     used by Four counted absences re-run against a second index, and all four hold
127. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProt Q03164 (KMT2A_HUMAN), subcellular location comments for the full-length protein and for the MLL cleavage products N320 and C180

     · UniProt 2026
     used by Four hours of MS67 in MV4;11, two KMT2A antibodies: the cheapest test of whether WRAD reaches the fusion or only wild-type KMT2A, The clock/SIRT1-regulated MLL1 acetylation site maps to KMT2A K1130 and K1133 in human numbering, just N-terminal to the CXXC and 208 residues before the breakpoint cluster - so it is retained in every KMT2A fusion, The N-over-C oncoprotein score is not fusion-specific by construction, because taspase1 cleaves wild-type KMT2A into an N320 and a C180 fragment that need not occupy the same chromatin - so a fusion-negative cell has a real N/C signal
128. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q8TF68 (ZN384_HUMAN) feature table, retrieved live 2026-09-24 by q173

     · UniProt Consortium 2026
     used by Four sources give ZNF384 three different zinc-finger counts - 8, 6 and 'five to eight' - and the paralogue's feature table explains where the 6 comes from, Last-exon indels that truncate the ZNF384 C-terminus phenocopy the fusion - so the fusion partner may not be the necessary element, The ZNF384 family is not the inverse of KMT2A::AFF1 - it is the SAME grammar written in the opposite gene order, and three of the four claims in the inverse framing are false, ZNF384 - a C2H2 transcription factor that is the invariant 3' half of a whole B-ALL fusion subtype, including AKAP8::ZNF384
129. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q5T0B9 (ZN362_HUMAN) feature table, retrieved live 2026-09-24 by q173 and read out in full alongside Q8TF68

     · UniProt Consortium 2026
     used by Four sources give ZNF384 three different zinc-finger counts - 8, 6 and 'five to eight' - and the paralogue's feature table explains where the 6 comes from, ZNF362 - the paralogue that makes the same leukaemia with the same partners, and that explains the six-zinc-finger convention
130. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     IntAct REST findInteractions/25609649 (Li et al. 2015), 4,119 records, and findInteractions/Q08050 (FOXM1), 145 records, fetched 2026-09-21

     · EMBL-EBI IntAct 2026
     used by FOXM1 - a one-panel MEN1 co-IP from a 4,119-row atlas, attached to a protein that is independently a validated MLL-rearranged leukaemia stem-cell dependency
131. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed esearch: MEN1[tiab] AND (FOXM1 OR "forkhead box M1")[tiab] = 0; menin[tiab] AND (FOXM1 OR "forkhead box M1")[tiab] = 5; FOXM1[tiab] AND (MLL OR KMT2A)[tiab] = 6; run 2026-09-21

     · NCBI PubMed 2026
     used by FOXM1 - a one-panel MEN1 co-IP from a 4,119-row atlas, attached to a protein that is independently a validated MLL-rearranged leukaemia stem-cell dependency
132. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9H334 (FOXP1_HUMAN), Forkhead box protein P1

     UniProt Consortium · UniProt 2026
     used by FOXP1 - the forkhead repressor that licenses the pro-B to pre-B transition and blocks apoptosis with NF-kB, sitting at a 105x MLL1-N bin in a leukaemia whose defining lesion is a pro-B arrest
133. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     HGNC record HGNC:3823 (FOXP1) and Ensembl gene ENSG00000114861 on GRCh37 and GRCh38

     HUGO Gene Nomenclature Committee; Ensembl · genenames.org / Ensembl 2026
     used by FOXP1 - the forkhead repressor that licenses the pro-B to pre-B transition and blocks apoptosis with NF-kB, sitting at a 105x MLL1-N bin in a leukaemia whose defining lesion is a pro-B arrest
134. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     Ensembl GRCh37 REST: lookup/id/ENSG00000114861?expand=1, per-transcript start coordinates and strand

     Ensembl · Ensembl GRCh37 archive 2026
     used by FOXP1 - the forkhead repressor that licenses the pro-B to pre-B transition and blocks apoptosis with NF-kB, sitting at a 105x MLL1-N bin in a leukaemia whose defining lesion is a pro-B arrest
135. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9C0B1 (FTO_HUMAN), human FTO, 505 aa

     · UniProt Consortium 2026
     used by FTO — highly expressed in MLL-rearranged AML, and the single flattest dependency row in this beat: 0.2% of 1,208 lines
136. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     NCBI PubMed esearch, bounded-absence query (counted negative)

     · NCBI E-utilities 2026
     used by FTSJ3 (Q8IY81) - the pre-rRNA 2'-O-methyltransferase at the weakest edge of the MLL-fusion nucleolar block: two baits of seven, not the index fusion, and never screened
137. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     UniProtKB - Q8IY81 (SPB1_HUMAN), pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3

     · UniProt Knowledgebase 2026
     used by FTSJ3 (Q8IY81) - the pre-rRNA 2'-O-methyltransferase at the weakest edge of the MLL-fusion nucleolar block: two baits of seven, not the index fusion, and never screened
138. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed entry Q9Y231 (FUT9_HUMAN)

     UniProt Consortium · UniProtKB 2026
     used by FUT9 - the dedicated Lewis-x synthase, structurally solved, and untouched by the KMT2A literature
139. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     HGNC record HGNC:4020 (FUT9)

     HUGO Gene Nomenclature Committee · HGNC 2026
     used by FUT9 - the dedicated Lewis-x synthase, structurally solved, and untouched by the KMT2A literature
140. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9Y231 (FUT9_HUMAN), O88819 (FUT9_MOUSE) and Q6P4F1 (OFUT3_HUMAN), SUBCELLULAR LOCATION comments with evidence codes and sources plus features and TISSUE SPECIFICITY, all fetched live 2026-09-21

     UniProt Consortium · Databases 2026
     used by FUT9 - the dedicated Lewis-x synthase, structurally solved, and untouched by the KMT2A literature
141. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O60861 (GAS7_HUMAN) Growth arrest-specific protein 7, Homo sapiens, 476 aa

     UniProt Consortium · UniProtKB 2026
     used by GAS7 — growth-arrest-specific F-BAR protein, the second pillar of the forced-oligomerisation model, KMT2A::GAS7 (MLL-GAS7), t(11;17)(q23;p13) — three patients, and the best mouse model in the partner class
142. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     IntAct molecular interaction database (EMBL-EBI), PSICQUIC tab27 record for id:P23771 AND id:Q8TEK3

     2026
     used by GATA3 - one of only two transcription-factor baits in a 109-bait BioID screen that recover DOT1L
143. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P23771 (GATA3_HUMAN)

     2026
     used by GATA3 - one of only two transcription-factor baits in a 109-bait BioID screen that recover DOT1L
144. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
     DepMap KMT2A-selective dependency scan over 17,728 genes: analyses/depmap-kmt2a-selective-scan-full/results.json, generated 2026-09-19. GATAD2A rank 866, difference -0.1144, mean_kmt2a_r -0.4062, mean_other -0.2918, pan_essentiality -0.3811.

     · DepMap via this repository 2026
     used by GATAD2A / p66-alpha (Q86YP4) - the subunit that bridges NuRD's two modules, the best-ranked NuRD gene in this project's KMT2A-selectivity scan, and present in the pan-fusion interactome under MLL-AF9 but NOT the index fusion
145. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     NCBI esearch via scripts/pubmed_safe.py on 2026-09-24. GATAD2A[tiab] AND MLL[tiab] -> 0 (translation "GATAD2A"[Title/Abstract] AND "MLL"[Title/Abstract]). GATAD2A[tiab] AND leukemia[tiab] -> 2 (PMIDs 40421803, 35681732). p66alpha[tiab] AND leukemia[tiab] -> 0. p66alpha[tiab] AND NuRD[tiab] -> 13. Positive control MEN1[tiab] AND MLL[tiab] -> 55.

     · NCBI PubMed E-utilities 2026
     used by GATAD2A / p66-alpha (Q86YP4) - the subunit that bridges NuRD's two modules, the best-ranked NuRD gene in this project's KMT2A-selectivity scan, and present in the pan-fusion interactome under MLL-AF9 but NOT the index fusion
146. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
     DepMap KMT2A-selective dependency scan over 17,728 genes: analyses/depmap-kmt2a-selective-scan-full/results.json, generated 2026-09-19. GATAD2B rank 2,141, difference -0.0715, mean_kmt2a_r -0.1828, mean_other -0.1113, pan_essentiality -0.1452.

     · DepMap via this repository 2026
     used by GATAD2B / p66-beta (Q8WXI9) - the NuRD scaffold with the broadest presence in the pan-MLL-fusion interactome, five of seven baits and still not the index fusion, and a haploinsufficiency syndrome that caps any therapeutic idea
147. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     NCBI esearch via scripts/pubmed_safe.py on 2026-09-24. GATAD2B[tiab] AND MLL[tiab] -> 0 (translation "GATAD2B"[Title/Abstract] AND "MLL"[Title/Abstract]). GATAD2B[tiab] AND KMT2A[tiab] -> 1 (38114583). GATAD2B[tiab] AND leukemia[tiab] -> 2 (39696784, 35685361). p66beta[tiab] AND NuRD[tiab] -> 6. Positive control MEN1[tiab] AND MLL[tiab] -> 55.

     · NCBI PubMed E-utilities 2026
     used by GATAD2B / p66-beta (Q8WXI9) - the NuRD scaffold with the broadest presence in the pan-MLL-fusion interactome, five of seven baits and still not the index fusion, and a haploinsufficiency syndrome that caps any therapeutic idea
148. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q99684 (GFI1_HUMAN) SUBCELLULAR LOCATION comment and note, fetched 2026-09-21

     UniProt Consortium · UniProtKB 2026
     used by GFI1 — the repressor that LSD1 inhibitors actually work through, and the scan hit whose literature points the opposite way
149. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paperPMID 42418681
     USP22 is a novel vulnerability regulating MEIS1 protein abundance and gene transcription in KMT2Ar acute leukemia

     Bröchtel S, Schneider C, Müller M, Villinger C, Plenge T, Gupta MK, et al. (Cremer A, senior author) · Blood 2026
     used by Giving the reopening conditions an owner, and the first run changes two decisions (run), KAT2A / GCN5 - the SAGA catalytic subunit that reaches this disease through its complex rather than through its own symbol, and whose only chemical tool degrades its paralogue too, MEIS1 — rate-limiting for MLL leukemia stem cells, a surviving co-dependency, and embryonic-lethal when removed, The unnamed KMT2A-rearranged B-ALL line is SEM, and the deposition says KMT2A::AFF1 in a genotype field, USP22 — a KMT2A-rearranged dependency that works through MEIS1 protein stability, and is not an interactor of the fusion
150. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     UniProtKB Q9BZE0 (GLIS2_HUMAN): sequence length, domain, zinc-finger, DNA-binding, repeat, motif and region features, and PDB cross-references

     UniProt Consortium · UniProtKB 2026
     used by GLIS2 (GLI-similar 2) domain architecture
151. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P00367 (DHE3_HUMAN), Glutamate dehydrogenase 1, mitochondrial — accession, primary gene name, length and subcellular-location comment retrieved 2026-09-24

     · UniProt Consortium, EMBL-EBI/SIB/PIR 2026
     used by GLUD1 is a hexameric mitochondrial matrix dehydrogenase recovered on 11 spectra with non-zero control signal from a nuclear pulldown — and this corpus has already declined one KMT2A partner whose sole source was a cryo-EM structure of GLUD1 — declined
152. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     NCBI PubMed esearch, bounded-absence query (counted negative)

     · NCBI E-utilities 2026
     used by GNL2 / Ngp-1 (Q13823) - a nucleostemin-family nucleolar GTPase in the MLL-fusion nucleolar block, in the index fusion's column at p = 0.0492, and the one member with a published granular-component assignment
153. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
     IntAct molecular interaction database, PSICQUIC MITAB 2.7, query id:Q08379 AND id:Q9UHB7, 3 rows retrieved 2026-09-21

     · IntAct (EMBL-EBI) 2026
     used by GOLGA2 (GM130) - a Golgi matrix protein with 249 partners in the one yeast screen that reported it binding AFF4, which had five
154. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q08379 (GOGA2_HUMAN, Golgin subfamily A member 2), subcellular location and function comments with evidence codes

     · UniProtKB/Swiss-Prot 2026
     used by GOLGA2 (GM130) - a Golgi matrix protein with 249 partners in the one yeast screen that reported it binding AFF4, which had five
155. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted-absence search for GOLGA2/GM130 against MLL, KMT2A and leukaemia, run 2026-09-21

     · PubMed (NCBI) 2026
     used by GOLGA2 (GM130) - a Golgi matrix protein with 249 partners in the one yeast screen that reported it binding AFF4, which had five
156. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     NCBI eutils esummary db=pubmed (ids 31202577,31202576,28735753,28794467,37788669,34405474), elink dbfrom=pubmed db=pmc id=31202576, esearch db=pmc on the title phrase; and Europe PMC REST search resultType=core by DOI, PMC/31202576/fullTextXML, and BODY: phrase search - all executed 2026-09-22

     NCBI E-utilities and EMBL-EBI Europe PMC REST · NCBI / Europe PMC 2026
     used by Gothe 2019's full text IS reachable - not through PMC, which has no deposit, but through an author search that surfaces the bioRxiv preprint; fourteen routes, and the two Europe PMC id links that look like a PMC record are both traps
157. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9NQX3 (GEPH_HUMAN) Gephyrin, Homo sapiens, 736 aa

     UniProt Consortium · UniProtKB 2026
     used by GPHN (gephyrin) — synaptic scaffold and molybdenum-cofactor enzyme, KMT2A fusion partner in t(11;14)(q23;q24), KMT2A::GPHN (MLL-gephyrin), t(11;14)(q23;q24) — the 15-residue counterexample
158. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q8TD30 (ALAT2_HUMAN), Alanine aminotransferase 2

     UniProt Consortium · UniProt 2026
     used by GPT2 (Q8TD30) - the EARLIEST-moving and third-most menin-selective gene in the serine arm, and the one REH cannot control because it is below the array floor there
159. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     genome-kmt2a-exon-11-ctcf-summit-measured and ana-kmt2a-bcr-ctcf-site-coordinate-overlap, this graph's own entries, read 2026-09-22; their primary sources are GEO GSE129526, ENCODE ENCSR000AKB and PMID 34405474 as recorded there

     · Iqbal Lab oncofusion knowledge graph 2026
     used by Gray 2023's own 'exon 11 CTCF site' in RPE cells, measured: centroid GRCh38 chr11:118,488,662-118,488,761, inside canonical exon 11 and 34 bp from the independently measured summit - the graph's CTCF adjudication is confirmed, not overturned
160. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI E-utilities esearch db=pubmed: KMT1A[tiab] = 22, KMT1A[tiab] AND KMT2A[tiab] = 0, KMT1A[tiab] AND MLL[tiab] = 0

     · NCBI PubMed 2026
     used by GSE139196: SUV39H1 ChIP-Seq in MCF-7 with and without 40 minutes of estradiol - a ligand-inducible SUV39H1 occupancy experiment, filed under the retired symbol KMT1A in its own sample titles, The GEO sweep that q110 named as free and did not run: SUV39H1 chromatin occupancy HAS been measured in two human cell types, six samples, hg38 bigWigs already deposited - so the writer half of the H3K9me3 absence is measured-not-analysed, not never-measured
161. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset
     GEO GSE210480 CTCF and H3K9me1 supplementary bigWigs compared by HTTP HEAD Content-Length and by exact per-base array equality over a 5 kb window, 2026-09-22; code and output at analyses/q108-gse210480-h3k9me3-kmt2a-bcr/followups.py and results_followups.json

     · NCBI Gene Expression Omnibus 2026
     used by GSE210480 carries FOUR CTCF bigWigs under EIGHT sample accessions, byte-identical, under different filenames - so counting GEO sample records doubled the replicate count and would have halved every standard error, RUN: the eight unreported H3K9me3 samples of GSE210480, read at the KMT2A CTCF element - H3K9me3 does not move where H3K9me1 moves 3.9-fold, and the me1/me2 positive controls passed, What is left after the missing arm was read: there is no H3K9me1, me2 or me3 measurement at the KMT2A breakpoint region in ANY haematopoietic cell, and the founding paper's own archive contains none because all 60 of its samples are epithelial
162. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.analysis
     GEO series GSE299100, sample titles and supplementary filenames enumerated via acc.cgi targ=gsm, fetched 2026-09-23; located by an NCBI GDS search over menin-inhibitor terms returning 112 series

     Oncofusion knowledge graph, coordinator · GEO deposit survey, reproducible 2026
     used by GSE299100 supplies the vehicle-versus-vehicle pair that neither GSE260742 nor GSE127507 could - two independent control hairpins, both DMSO, same date, uniformly processed to hg38_rmdup.tdf, for MEN1, MLL1 and input - in MV4-11, which Cellosaurus confirms carries KMT2A::AFF1 though it presents as monocytic rather than the infant B-ALL this project studies. It also holds MEN1 and MLL1 ChIP under five different menin inhibitors in that line, and the six control files total 1.87 GB, In human KMT2A::AFF1 MV4;11 (monocytic, not B-lineage), the vehicle-versus-vehicle noise floor is 9.4% at the top 0.1% of menin/MLL1 sites and 0.1-2.6% in every other stratum - so cycle 102's borrowed 4-10% band is about right AT THE PEAKS and four to five times too generous everywhere else, and it was applied everywhere
163. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 41399259
     Targeting IMPDH to inhibit SAMHD1 in KMT2A-rearranged leukaemia.

     Klootsema Y, Tsesmetzis N, Sharma S, ..., Herold N · Cell Cycle 2026
     used by Guanine nucleotide supply sustains the LEDGF/menin/MLL-fusion complex - the one place in this graph where metabolism sits UPSTREAM of the menin interface, IMPDH2 - the rate-limiting guanine-nucleotide enzyme whose inhibition lowers LEDGF and menin protein and dismantles the MLL-fusion complex itself, Is the metabolic phenotype a consequence of the fusion programme or an independent dependency? The answer is that BOTH directions are published, and one of them points the other way entirely, Repurposing approved IMPDH inhibitors (mycophenolate, mizoribine, ribavirin) in KMT2A-rearranged leukaemia - cheap, mechanistically attractive, and asking an immunosuppressant of a neutropenic infant, SAMHD1 - the dNTP hydrolase that is the real biomarker behind the IMPDH story, and the reason the KMT2A framing of that story does not hold, The experiment that separates lineage from ontogeny: one KMT2A fusion, two cell-of-origin contexts, three metabolic perturbations, and a limiting-dilution readout alongside the viability one, The myeloid/lymphoid metabolic split in KMT2A-rearranged leukaemia is set by CELL OF ORIGIN (fetal versus adult), not by lineage or by the fusion partner
164. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 41711315
     IMPDH inhibition enhances cytarabine efficacy in SAMHD1-expressing leukaemia cells via guanine nucleotide depletion.

     Yague-Capilla M, Dirks C, Eiden C, ..., Rudd SG · Mol Oncol 2026
     used by Guanine nucleotide supply sustains the LEDGF/menin/MLL-fusion complex - the one place in this graph where metabolism sits UPSTREAM of the menin interface, IMPDH2 - the rate-limiting guanine-nucleotide enzyme whose inhibition lowers LEDGF and menin protein and dismantles the MLL-fusion complex itself, Repurposing approved IMPDH inhibitors (mycophenolate, mizoribine, ribavirin) in KMT2A-rearranged leukaemia - cheap, mechanistically attractive, and asking an immunosuppressant of a neutropenic infant, SAMHD1 - the dNTP hydrolase that is the real biomarker behind the IMPDH story, and the reason the KMT2A framing of that story does not hold
165. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 41191529
     Guanine nucleotides drive ribosome biogenesis and glycolytic reprogramming in acute myeloid leukemia stem cells.

     Kawano G, Ikeda R, Ishihara D, ..., Kikushige Y · Blood 2026
     used by Guanine nucleotide supply sustains the LEDGF/menin/MLL-fusion complex - the one place in this graph where metabolism sits UPSTREAM of the menin interface, IMPDH2 - the rate-limiting guanine-nucleotide enzyme whose inhibition lowers LEDGF and menin protein and dismantles the MLL-fusion complex itself
166. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     HGNC records for H2AZ1 (HGNC:4741) and H2AZ2 (HGNC:20664) and the UniProt records P0C0S5 (H2AZ_HUMAN, 128 aa) and Q71UI9 (H2AV_HUMAN, 128 aa), fetched live 2026-09-20 with gene_primary read back on every row

     · HUGO Gene Nomenclature Committee / UniProt 2026
     used by H2A.Z - two genes of identical length, one KMT2A paper, and the measured quantity is a ratio nobody has repeated
167. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Word-boundary sweep for H2A.Z, H2AZ1, H2AZ2, H2AFZ and H2AFV across nineteen full texts of the core KMT2A-rearranged chromatin literature, retrieved through the PMC HTML and Europe PMC fullTextXML routes and stripped tags-first, entities-second

     · PubMed Central / Europe PMC 2026
     used by H2A.Z - two genes of identical length, one KMT2A paper, and the measured quantity is a ratio nobody has repeated, H3.3 - the graph's most-named epigenetic object with no entry, 325 mentions, and not one measurement in a KMT2A-rearranged cell, Rule 80 measured: the abstract index missed the best KMT2A measurement for three marks out of seven, and confirmed the absence for the other four
168. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P16104 (H2AX_HUMAN), Histone H2AX, 143 aa, primary gene name H2AX, synonym H2AFX

     · UniProt Consortium 2026
     used by H2AX - filed as a gene and not as a mark, and the reason that decision changes what the graph can say
169. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P0C0S5 (H2AZ_HUMAN), Histone H2A.Z, 128 aa

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by H2AZ1 - the one histone variant with a direct KMT2A-fusion paper: MLL-AF10 and MLL-ENL recruit Tip60 to Hoxa9 to acetylate H2A.Z
170. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     HGNC records for H3-3A (HGNC:4764) and H3-3B (HGNC:4765), and the UniProt record P84243 (H33_HUMAN, 136 aa), fetched live 2026-09-20 with gene_primary read back

     · HUGO Gene Nomenclature Committee / UniProt 2026
     used by H3.3 - the graph's most-named epigenetic object with no entry, 325 mentions, and not one measurement in a KMT2A-rearranged cell
171. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     UniProtKB - P68431 (H31_HUMAN), Histone H3.1, and IntAct PSICQUIC MITAB2.7 rows for Q03164, O00255, O75475 and Q9UHB7

     · UniProt Knowledgebase / EMBL-EBI IntAct 2026
     used by H3C1 stays rejected, and now with the two numbers the registry row lacked: its accession carries TEN gene names, and removing every substrate and ribosome symbol moves interactome coverage 43.8% -> 46.1%
172. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed esearch counts for histone-mark queries in KMT2A-rearranged leukaemia, run 2026-09-20

     · NCBI PubMed 2026
     used by H3K36me2/3 - the mark that physically switches PRC2 off, that LEDGF reads to reach chromatin, and that a comparator fusion uses to keep EZH2 off HOXA
173. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed esearch counts for histone-mark queries in KMT2A-rearranged leukaemia, run 2026-09-20

     · NCBI PubMed 2026
     used by H3K4me3 - the mark KMT2A's own SET domain writes, that the fusion cannot write, that an interface in this graph already binds, and that switches PRC2 off
174. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 42424456
     Degron-independent recruitment of KAT2A expands the target space of CRBN molecular glues.

     Ojeda S; Wang M; Baek K; Bourgeois W; Sommerschield A; Yue H; et al. · Science 2026
     used by H3K9ac - the mark KMT2A fusions pile up on their own targets, the one the AF9 reader actually binds, and the one a DOT1L inhibitor strips off first
175. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.preprintPMID 42523331
     Disrupting a Convergent Acetylation Circuit Collapses Leukemic Identity Across AML Subtypes.

     Deshpande A; Chiang CY; Perales M; Niranjan N; Sinha N; Finlay D; et al. · bioRxiv 2026
     used by H3K9ac - the mark KMT2A fusions pile up on their own targets, the one the AF9 reader actually binds, and the one a DOT1L inhibitor strips off first, KAT2A / GCN5 - the SAGA catalytic subunit that reaches this disease through its complex rather than through its own symbol, and whose only chemical tool degrades its paralogue too, KAT2B / PCAF - named in an existing entry's own id and never written, and the only acetyltransferase in this graph whose substrate is a fusion partner protein
176. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     UniProtKB Q9H9B1 (EHMT1_HUMAN, 1,298 aa) FUNCTION comment, read against Q96KQ7 (EHMT2_HUMAN, 1,210 aa); both resolved by gene_exact + organism_id:9606 + reviewed:true returning exactly one row each, with the primary gene name read back

     · UniProt Consortium 2026
     used by H3K9me1 - the only H3K9 state whose level at the KMT2A breakpoint cluster region has ever been measured, and it is LOW there until KDM3B is removed, H3K9me2 - named sixty times in this graph with no entry of its own, the mark that defines the lamina-associated domains the fusion's targets sit beside, and the only H3K9 methylation state ever measured at a KMT2A fusion's own binding sites
177. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     UniProtKB Q03112 (MECOM_HUMAN, 1,230 aa) FUNCTION comment; resolved by gene_exact:MECOM AND organism_id:9606 AND reviewed:true returning one row, primary gene name MECOM read back, length 1,230 checked

     · UniProt Consortium 2026
     used by H3K9me1 - the only H3K9 state whose level at the KMT2A breakpoint cluster region has ever been measured, and it is LOW there until KDM3B is removed
178. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     UniProtKB Q9Y4C1 (KDM3A_HUMAN, 1,321 aa) FUNCTION comment; resolved by gene_exact:KDM3A AND organism_id:9606 AND reviewed:true returning one row with primary gene name KDM3A

     · UniProt Consortium 2026
     used by H3K9me1 - the only H3K9 state whose level at the KMT2A breakpoint cluster region has ever been measured, and it is LOW there until KDM3B is removed, H3K9me2 - named sixty times in this graph with no entry of its own, the mark that defines the lamina-associated domains the fusion's targets sit beside, and the only H3K9 methylation state ever measured at a KMT2A fusion's own binding sites
179. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q7LBC6 (KDM3B_HUMAN) FUNCTION, CATALYTIC ACTIVITY and feature table; resolved 2026-09-22 by gene_exact:KDM3B AND organism_id:9606 AND reviewed:true returning exactly one row, primary gene name KDM3B and length 1,761 read back

     · UniProt Consortium 2026
     used by H3K9me1 - the only H3K9 state whose level at the KMT2A breakpoint cluster region has ever been measured, and it is LOW there until KDM3B is removed, KDM3B - the H3K9me1/2 demethylase that sits on the KMT2A breakpoint cluster region and keeps it from rearranging, and the only leukaemia gene in this graph whose direction of effect flips between the myeloid and the lymphoid literature
180. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed esearch counts, querytranslations and warninglists for H3R2me2a in KMT2A-rearranged leukaemia, run twice 2026-09-22

     · NCBI PubMed 2026
     used by H3R2me2a - the asymmetric arginine mark two residues from H3K4 that LOCKS the WRAD module off the histone tail, and the first arginine mark node in this graph
181. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed esearch counts, querytranslations, warninglists and PMID set comparisons for H3R2 methylarginine states, run twice 2026-09-22

     · NCBI PubMed 2026
     used by H3R2me2s - the symmetric mark on the SAME residue as H3R2me2a, which permits rather than enhances WRAD access, and whose 'enhancing' half this graph inherited from the paper that was later revised
182. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9NVM4 (ANM7_HUMAN) - protein arginine methyltransferase 7, FUNCTION, CATALYTIC ACTIVITY, SUBCELLULAR LOCATION and domain feature table, read back 2026-09-22

     · UniProt 2026
     used by H3R2me2s - the symmetric mark on the SAME residue as H3R2me2a, which permits rather than enhances WRAD access, and whose 'enhancing' half this graph inherited from the paper that was later revised, H4R3me2s - the repressive symmetric arginine mark that recruits DNMT3A, blocks a KMT2 enzyme's own PHD module, and is the ONLY arginine mark ever measured in a KMT2A-fusion system, PRMT7 - the enzyme whose class is still disputed, which represses a KMT2 enzyme by writing H4R3me2s, which is required for leukaemia stem cells in CML, and whose only H3R2 claim is the one this beat was dispatched to check
183. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed records 34669117, 35435596, 28440495, 34745943 and 25065740, retrieved by H4K20me1[tiab] AND leukemia[tiab] (querytranslation: "H4K20me1"[Title/Abstract] AND "leukemia"[Title/Abstract]) and read as abstracts on 2026-09-23

     · NCBI PubMed 2026
     used by H4K20me1 - the transcription- and replication-linked H4 state, whose gene-body level tracks Pol II; it HAS been profiled genome-wide in human haematopoietic stem cells twice, and a query scoped to 'leukemia' cannot see either dataset
184. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI E-utilities esearch db=pubmed via scripts/pubmed_safe.py on 2026-09-23; representative querytranslation "H4K20me1"[Title/Abstract] AND "KMT2A"[Title/Abstract]; each operand separately tagged, no parenthesised group carrying a [tiab] tag, and the KMT2A operand always paired with a separate MLL run

     · NCBI PubMed 2026
     used by H4K20me1 - the transcription- and replication-linked H4 state, whose gene-body level tracks Pol II; it HAS been profiled genome-wide in human haematopoietic stem cells twice, and a query scoped to 'leukemia' cannot see either dataset
185. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI PubMed esearch, bounded-absence queries with querytranslation and warninglist recorded

     · NCBI E-utilities 2026
     used by H4K20me2 - the abundant repair-linked H4 mark, the 53BP1 docking site, and the first H4K20 state in this graph; never once measured in a KMT2A-rearranged cell
186. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q99873 (ANM1_HUMAN) - protein arginine N-methyltransferase 1, FUNCTION comment block, read back 2026-09-22

     · UniProt 2026
     used by H4R3me2a - the activating arginine mark that a KMT2-family enzyme's OWN tandem PHD module reads, where the Kabuki-syndrome mutations sit, and which no KMT2A-fusion study has ever measured, PRMT1 — an MLL-fusion cofactor whose first-in-human inhibitor was terminated for lack of efficacy and toxicity
187. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed esearch counts, querytranslations, warninglists and PMID set comparisons for H4R3 methylarginine states, run twice 2026-09-22

     · NCBI PubMed 2026
     used by H4R3me2a - the activating arginine mark that a KMT2-family enzyme's OWN tandem PHD module reads, where the Kabuki-syndrome mutations sit, and which no KMT2A-fusion study has ever measured
188. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O14744 (ANM5_HUMAN) - protein arginine N-methyltransferase 5; record as read back 2026-09-22 and as recorded in this graph's gene-prmt5 entry

     · UniProt 2026
     used by H4R3me2s - the repressive symmetric arginine mark that recruits DNMT3A, blocks a KMT2 enzyme's own PHD module, and is the ONLY arginine mark ever measured in a KMT2A-fusion system, PRMT5 - the type II arginine methyltransferase this graph has reached for sixteen times, whose mark on H3R2 RECRUITS WDR5 to chromatin
189. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed esearch counts, querytranslations, warninglists and PMID set comparisons for H4R3me2s in KMT2A-rearranged leukaemia, run twice 2026-09-22

     · NCBI PubMed 2026
     used by H4R3me2s - the repressive symmetric arginine mark that recruits DNMT3A, blocks a KMT2 enzyme's own PHD module, and is the ONLY arginine mark ever measured in a KMT2A-fusion system
190. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.trial_registry
     A Phase I Study of SNDX 5613 (Revumenib) as Post-Transplant Maintenance After Allogeneic Hematopoietic Cell Transplant in Patients With KMT2A-Rearranged or NPM1-Mutated Acute Leukemia

     City of Hope Medical Center · ClinicalTrials.gov 2026
     used by Haematopoietic stem cell transplant in KMT2A-rearranged infant leukemia — what it is for, and why most children who need it never get it
191. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Gene Ontology and Cell Ontology term records retrieved via the EBI Ontology Lookup Service (OLS4) API

     Gene Ontology Consortium; Cell Ontology; EMBL-EBI Ontology Lookup Service · Databases 2026
     used by Haemogenic endothelium — the vessel-wall cell that gives birth to blood
192. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     GEO series GSE260742 / GSE260456 (Neville) and GSE249076 / GSE249078 (Zhou), supplementary file listings and sizes retrieved from the NCBI GEO FTP

     · NCBI Gene Expression Omnibus 2026
     used by Half the 'free' PRC1.1 intersection really was free: Zhou's locus set is a publisher table, Neville's does not exist, and only that half costs 25 GB
193. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
     zhou-locus-set-join: this graph's gene entries joined onto Zhou supplemental Table 4, with symbol resolution gated on the project's symbol-collisions registry

     · Oncofusion knowledge graph (internal analysis) 2026
     used by Half the PRC1.1 intersection was free all along: Zhou's locus set is a publisher supplementary table, and 159 of this graph's gene entries are in it
194. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.analysis
     Load-ranking of unopposed claims in the Oncofusion knowledge graph

     · Oncofusion knowledge graph (internal analysis) 2026
     used by Half this graph's claims are unopposed; these are the ones that matter
195. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Cellosaurus cell line HB11;19 (CVCL_8227)

     Bairoch A, et al.; Cellosaurus · Cellosaurus (SIB) 2026
     used by HB11;19 (CVCL_8227) keeps the YEATS domain and expresses both derivative transcripts - so it is the reciprocal-POSITIVE t(11;19) line, and there is no negative one, The reciprocal MLLT1::KMT2A transcript was reported in the paper that discovered KMT2A, and nobody has gone back to it in thirty-four years
196. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted-absence search for HCFC2 against KMT2A/MLL/menin, run 2026-09-20

     · PubMed (NCBI) 2026
     used by HCFC2 — menin's other host cell factor, present in the founding paper by gel filtration and never mentioned again
197. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q9Y5Z7 (HCFC2_HUMAN, Host cell factor 2)

     · UniProtKB/Swiss-Prot 2026
     used by HCFC2 — menin's other host cell factor, present in the founding paper by gel filtration and never mentioned again
198. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q13547 (HDAC1_HUMAN), Histone deacetylase 1

     UniProt Consortium · UniProtKB, retrieved 2026-09-20 2026
     used by HDAC1 - a class I eraser that has no dependency claim of its own in this disease, because removing it alone does nothing until HDAC2 goes too
199. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q92769 (HDAC2_HUMAN), Histone deacetylase 2

     UniProt Consortium · UniProtKB, retrieved 2026-09-20 2026
     used by HDAC2 - the buffering half of the class I pair, and the one class I enzyme a drug result in acute leukaemia has actually been pinned to, in AML rather than in a KMT2A fusion
200. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O15379 (HDAC3_HUMAN), Histone deacetylase 3

     UniProt Consortium · UniProtKB, retrieved 2026-09-20 2026
     used by HDAC3 - the only HDAC in this disease whose requirement was established genetically rather than by a drug, and the same experiment shows it is not fusion-specific
201. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9UQL6 (HDAC5_HUMAN), Histone deacetylase 5

     UniProt Consortium · UniProtKB, retrieved 2026-09-20 2026
     used by HDAC5 - the eraser in an existing entry's own id, and the one HDAC in this graph that erases a mark on a fusion partner protein rather than on a histone
202. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9UQL6 (HDAC5_HUMAN) - SUBCELLULAR LOCATION comment block with evidence codes

     · UniProt Consortium 2026
     used by HDAC5 - the eraser in an existing entry's own id, and the one HDAC in this graph that erases a mark on a fusion partner protein rather than on a histone
203. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 41608562
     CK2-mediated HDAC5 shuttling regulates DNA end resection through Ku70 deacetylation.

     Liang X, Zhao J, Li S, Wei R, Yu H, Zhang Q, Fu Q, Qin G, Zhao Y, Liu J, Liu Z, Peng T, Meng J, Gou S, Yin T, Wu H, Wang B, Zhou Y · Theranostics 2026
     used by HDAC5 - the eraser in an existing entry's own id, and the one HDAC in this graph that erases a mark on a fusion partner protein rather than on a histone
204. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.journal-articlePMID 41701111
     Discovery of Potent HDAC6-Selective Inhibitors Based on Artemisinin: Design, Synthesis, and Antitumor Evaluation

     · J Med Chem 2026
     used by HDAC6 - the one HDAC family member this graph refused, whose refusal named a falsifier that has been in the literature since 2020 and fires in the index fusion's own cell line
205. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB REST search, gene_exact:HDAC7 AND organism_id:9606 AND reviewed:true, with fields accession,id,gene_primary,gene_synonym,protein_name,length; and UniProtKB records Q9UKV0 and Q8WUI4

     UniProt Consortium · UniProtKB, retrieved 2026-09-20 2026
     used by HDAC7 - the eraser the index fusion silences, where the proposed therapy is to INDUCE the HDAC, and two 2024-2025 papers point in opposite directions, No HDAC-inhibitor result in this disease attributes to an HDAC enzyme - the only per-enzyme evidence is genetic, and it says the enzyme is not fusion-specific
206. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9UKV0 (HDAC9_HUMAN), Histone deacetylase 9

     UniProt Consortium · UniProtKB, retrieved 2026-09-20 2026
     used by HDAC9 - the only HDAC with a KMT2A-rearrangement expression signature across 211 paediatric patients, and it is high, prognostic, and independent of partner and lineage
207. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch: (MLL[tiab] OR KMT2A[tiab]) AND HDAC9[tiab], run 2026-09-20, count 3, all three title-checked by efetch (29978456, 38053201, 36776851)

     NCBI E-utilities · PubMed 2026
     used by HDAC9 - the only HDAC with a KMT2A-rearrangement expression signature across 211 paediatric patients, and it is high, prognostic, and independent of partner and lineage
208. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9UKV0 (HDAC9_HUMAN) - SUBCELLULAR LOCATION comment block with evidence codes

     · UniProt Consortium 2026
     used by HDAC9 - the only HDAC with a KMT2A-rearrangement expression signature across 211 paediatric patients, and it is high, prognostic, and independent of partner and lineage
209. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI PubMed esearch, alias-expanded bounded query for HDAC9 in KMT2A-rearranged leukaemia, run 2026-09-21

     · NCBI E-utilities 2026
     used by HDAC9 - the only HDAC with a KMT2A-rearrangement expression signature across 211 paediatric patients, and it is high, prognostic, and independent of partner and lineage
210. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     IntAct molecular interaction database (EMBL-EBI), PSICQUIC tab27 record for id:O75475 AND id:P51858

     2026
     used by HDGF - the third PWWP paralogue, which pulls down LEDGF but has the reader domain WITHOUT the domain that grips MLL
211. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P51858, O75475 and Q7Z4V5 domain and region feature tables

     2026
     used by HDGF - the third PWWP paralogue, which pulls down LEDGF but has the reader domain WITHOUT the domain that grips MLL
212. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q7Z4V5 (HDGR2_HUMAN), Hepatoma-derived growth factor-related protein 2, synonyms HDGF2, HDGFRP2, HRP2, 671 aa

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by HDGFL2 / HRP-2 - the second IBD protein, which binds KMT2A at the same site with the same affinity and does NOT need menin to do it
213. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P54198 (HIRA_HUMAN), Protein HIRA, 1017 aa

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by HIRA - the chaperone that puts new H3.3 into transcribed gene bodies, and therefore the machine that runs this graph's clearance clock
214. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P84243 (H33_HUMAN), Histone H3.3, 136 aa, gene names H3-3A; H3-3B

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by Histone H3.3 - one protein, two genes, and the reason this graph should not file it as gene-h3f3a
215. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed human entry P04439 (HLAA_HUMAN)

     UniProt Consortium · UniProtKB 2026
     used by HLA-A - the class I heavy chain a menin inhibitor was actually measured on, and the human orthologue of the MHC class I molecule that protects MLL-AF9 leukaemia stem cells from NK cells
216. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P04439 (HLAA_HUMAN) SUBCELLULAR LOCATION comment, fetched 2026-09-21

     · UniProt Consortium 2026
     used by HLA-A - the class I heavy chain a menin inhibitor was actually measured on, and the human orthologue of the MHC class I molecule that protects MLL-AF9 leukaemia stem cells from NK cells
217. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     Human Protein Atlas v25.1, subcellular (immunofluorescence) and Blood Atlas records for HLA-A, fetched 2026-09-21

     · Human Protein Atlas 2026
     used by HLA-A - the class I heavy chain a menin inhibitor was actually measured on, and the human orthologue of the MHC class I molecule that protects MLL-AF9 leukaemia stem cells from NK cells
218. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed human entry P01889 (HLAB_HUMAN)

     UniProt Consortium · UniProtKB 2026
     used by HLA-B - the class I heavy chain the bivalency screen was actually read out on, and the locus that presents the one KMT2A epitope this graph has a structure for
219. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P01889 (HLAB_HUMAN), SUBCELLULAR LOCATION comment with evidence codes and sources plus the signal-peptide and transmembrane features, fetched live 2026-09-21

     UniProt Consortium · Databases 2026
     used by HLA-B - the class I heavy chain the bivalency screen was actually read out on, and the locus that presents the one KMT2A epitope this graph has a structure for
220. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed entry P01911 (DRB1_HUMAN)

     UniProt Consortium · UniProtKB 2026
     used by HLA-DR - a two-chain MHC class II heterodimer, so no single gene symbol denotes the surface marker a flow report calls HLA-DR, HLA-DRB1 - the polymorphic beta chain, one of several that can make an HLA-DR dimer, and the reason a chain cannot be inferred from a flow result
221. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     UniProtKB Q16534 (HLF_HUMAN): sequence length, domain, zinc-finger, DNA-binding, repeat, motif and region features, and PDB cross-references

     UniProt Consortium · UniProtKB 2026
     used by HLF (hepatic leukemia factor) domain architecture
222. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P41235 (HNF4A_HUMAN), Hepatocyte nuclear factor 4-alpha

     UniProt Consortium · UniProt 2026
     used by HNF4A - a liver and pancreas nuclear receptor acting as the metabolic effector of TIFAB in KMT2A::MLLT3 AML, on a single paper
223. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P22626 (ROA2_HUMAN), human HNRNPA2B1, 353 aa

     · UniProt Consortium 2026
     used by HNRNPA2B1 — the panel's strongest KMT2A-selective RNA-layer gene after PTBP1, with ZERO records against MLL or KMT2A
224. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.analysis
     analyses/is-the-floor-a-property-of-the-mark/run.py and results.json, this repository, computed 2026-09-23 with zero downloads from binned tracks in C:/Temp/q135 and the FLAG DMSO stratifier in C:/Temp/q117; replicate identity and confound structure from analyses/what-the-deposit-says-its-channels-are and the Q135 beat

     Oncofusion knowledge graph, coordinator · internal analysis, reproducible from the repository 2026
     used by Holding mark, arm and drug conditions fixed and varying only which confound the replicate pair carries: the floor ranges are DISJOINT at D1 and D10, a processing-confounded pair inflates D1 2.20x while a batch-confounded pair inflates D10 2.21x, and the direction reverses by stratum - so the floor is a property of the pair, not of the mark or the arm, and every floor this project has published came from the pair type that is wrong for D1
225. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed database queries 'HOTAIRM1 AND leukemia' (23 records) and 'HOTAIRM1 AND leukemia AND MLL AND KMT2A' (0 records), executed 2026-09-18

     National Library of Medicine, PubMed · PubMed 2026
     used by HOTAIRM1 lncRNA — the myeloid-differentiation transcript at the 3' end of HOXA, with a KMT2A-r evidence gap
226. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Ensembl REST API gene lookup, homo_sapiens, assembly GRCh38

     Ensembl / EMBL-EBI · Ensembl 2026
     used by HOTAIRM1 lncRNA — the myeloid-differentiation transcript at the 3' end of HOXA, with a KMT2A-r evidence gap
227. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Ensembl REST API gene lookup, homo_sapiens, assembly GRCh38 (release 114)

     Ensembl / EMBL-EBI · Ensembl 2026
     used by HOTTIP lncRNA — the 5' HOXA switch that holds the leukemic chromatin domain open
228. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB - O14980 (XPO1_HUMAN), Exportin-1

     UniProt Consortium · UniProtKB 2026
     used by How a lift operator became a postal address: the idea behind the XPO1 axis, in plain language, Two pools of one protein: the chromatin-bound XPO1 that matters here has never been separated biochemically from the soluble export machine, XPO1 / exportin-1 (CRM1) - the cell's main nuclear export receptor, and a chromatin-bound transcriptional scaffold, XPO1 mRNA goes UP when you inhibit the protein - the pharmacodynamic marker that made the paediatric trial interpretable, and what it cannot tell you
229. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     RCSB PDB entry 1PUF, polymer entity records 1-4; and UniProt REST records P09631, P40424, P31269, P40426

     RCSB Protein Data Bank; UniProt Consortium; queried by this project 2026-09-20 · Structural and sequence databases 2026
     used by How HOXA9 binds DNA: a hexapeptide into a PBX pocket, a 1.9 A structure that is mouse HoxA9 plus human Pbx1 homeodomains, and a second route that makes the motif redundant
230. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.analysis
     Partner-provenance audit: how much of this graph's mechanism comes from a fusion that is not KMT2A::AFF1

     · Oncofusion knowledge graph (internal analysis) 2026
     used by How much of this graph's mechanism is somebody else's fusion? A counted answer: 54% of fusion-bearing evidence, and 0% from a dedicated human KMT2A::AFF1 experiment
231. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     ENCODE portal: /targets/BARD1-human/ 200 and /targets/RAD50-human/ 200; /search/?type=Experiment&status=released&target.label=BARD1&assay_title=TF+ChIP-seq returns 404 while the same search without the assay filter returns 2 CRISPR RNA-seq experiments

     · ENCODE Project 2026
     used by How the three occupancy archives spell zero: ENCODE 404, ReMap 401, ChIP-Atlas 404 - and ChIP-Atlas spells a one-character URL typo exactly the same way, so a whole sweep can come back cleanly and be entirely false
232. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     ReMap 2022 API findByTarget: BARD1 401 {"error":"Sorry. There is no experiment for target BARD1 and tax_id 9606 on remap2022"}; SUV39H1 401; EXO1 401; CTCF 200, 172,276 bytes

     · ReMap 2026
     used by How the three occupancy archives spell zero: ENCODE 404, ReMap 401, ChIP-Atlas 404 - and ChIP-Atlas spells a one-character URL typo exactly the same way, so a whole sweep can come back cleanly and be entirely false
233. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     ChIP-Atlas hg38 target tables: CTCF.5.tsv 200 (47,217 bytes), CTCF.1.tsv 200, CTCF.10.tsv 200, CTCF.05.tsv 404; SUV39H1.5.tsv 200 with 4 SRX; BARD1.5.tsv 404; EXO1.5.tsv 404

     · ChIP-Atlas / DBCLS 2026
     used by How the three occupancy archives spell zero: ENCODE 404, ReMap 401, ChIP-Atlas 404 - and ChIP-Atlas spells a one-character URL typo exactly the same way, so a whole sweep can come back cleanly and be entirely false
234. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     ChIP-Atlas SUV39H1.5.tsv header: SRX7030945|MCF-7, SRX7030946|MCF-7, SRX7030947|MCF-7, SRX7030948|MCF-7

     · ChIP-Atlas / DBCLS 2026
     used by How the three occupancy archives spell zero: ENCODE 404, ReMap 401, ChIP-Atlas 404 - and ChIP-Atlas spells a one-character URL typo exactly the same way, so a whole sweep can come back cleanly and be entirely false, The GEO sweep that q110 named as free and did not run: SUV39H1 chromatin occupancy HAS been measured in two human cell types, six samples, hg38 bigWigs already deposited - so the writer half of the H3K9me3 absence is measured-not-analysed, not never-measured, Three archives, one answer: SUV39H1 has no ENCODE target record under any label (three routes, all empty), ChIP-Atlas's entire hg38 SUV39H1 holding IS the four GSE139196 MCF-7 samples re-indexed, and KMT2A is not among the 26 genes ChIP-Atlas calls SUV39H1 targets
235. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Ensembl REST API gene lookup, homo_sapiens, assembly GRCh38 (HOXA-AS2, HOXA-AS3, HOXA3, HOXA5, HOXA6)

     Ensembl / EMBL-EBI · Ensembl 2026
     used by HOXA-AS2 and HOXA-AS3 — mid-cluster antisense transcripts with essentially no KMT2A-r evidence
236. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed database queries 'HOXA-AS3' (37 records), 'HOXA-AS3 AND leukemia/myeloid' (0 records) and 'HOXA-AS2 AND leukemia' (8 records), executed 2026-09-18

     National Library of Medicine, PubMed · PubMed 2026
     used by HOXA-AS2 and HOXA-AS3 — mid-cluster antisense transcripts with essentially no KMT2A-r evidence
237. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P31260 (HXA10_HUMAN) - SUBCELLULAR LOCATION comment block with evidence codes

     · UniProt Consortium 2026
     used by HOXA10 - named in 27 entries as part of the HOXA output and never written; a posterior HOX paralogue that is regulated with HOXA9 and tested far less often
238. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42505395
     Fusion Gene KMT2A::SEPTIN6 in Acute Myeloid Leukemia Cell Line KOPM-88

     Nagel S, Meyer C, Kaufmann M, Fähnrich S, Rand U, Pommerenke C, MacLeod RAF, Eberth S · Cells 15(14):1286 2026
     used by HOXA7 - the one HOXA paralogue besides HOXA9 with a published loss-of-function requirement for MLL-fusion transformation, and the requirement was shown in vitro only
239. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     RCSB PDB entry 1PUF polymer-entity records and structure search against UniProt P31269 (zero results), retrieved via the RCSB data and search APIs

     RCSB Protein Data Bank; UniProt Consortium · Databases 2026
     used by HOXA9 — required for survival of established MLL-rearranged leukemia, and dispensable for starting it
240. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.paperPMID 42589252
     Effect of the Proteasome Inhibitor, Bortezomib, on Histone Modifications in Human Leukemic Cell Lines.

     Sattarifard H, Oyeyode M, Prajapati D, et al. · Int J Mol Sci 2026
     used by HOXA9 — required for survival of established MLL-rearranged leukemia, and dispensable for starting it
241. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P31269 (HXA9_HUMAN) - subcellular location with evidence codes, fetched 2026-09-20

     UniProt Consortium · UniProtKB 2026
     used by HOXA9 has its own nuclear bodies, and in monocytic AML they move into the eIF4E body - a subnuclear switch measured in patient marrow and never genotyped
242. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P35453, Homeobox protein Hox-D13 (HOXD13)

     UniProt Consortium · UniProtKB 2026
     used by HOXD13 domain architecture (UniProt P35453), NUP98::HOXD13, t(2;11)(q31;p15) — the myelodysplasia fusion, and a warning against targeting p53
243. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
     ana-q37-the-kmt2a-exon-11-anchor-carries-a-cbx3-and-a-brca1-peak-that-idr-removes

     Q37-archive-sweep · this graph 2026
     used by HP1-gamma holds a constitutive, sub-threshold foothold on the KMT2A exon-11 CTCF anchor in undamaged cells - the CTCF-primed model's missing resting state - and the reason nobody has seen it is that it sits below the reproducibility filter every public peak set applies
244. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.analysis
     menin-dna-repair-occupancy: GO DNA repair and homologous recombination gene sets tested against Zhou supplemental Table 4 by permutation

     · Oncofusion knowledge graph (internal analysis) 2026
     used by HR genes are menin-bound at 1.76x and so is ribosome biogenesis at 1.78x: the pathway-specific reading does not survive its own control
245. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     NCBI GEO DataSets esearch and analyses/what-the-citation-index-cannot-see/run.py, both run 2026-09-23

     Q139 · NCBI GEO / Iqbal Lab oncofusion knowledge graph repository 2026
     used by HTAN KMT2A-r ALL single-cell multiome — 25 patients (18 infants), scRNA-seq + scATAC-seq + snmC-seq2, with 2 paired pre/post lineage-switch cases and analysis code on GitHub
246. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
     analyses/hunting-the-discarded-spike-in/run.py and results.json, this repository; PMID 31821784 esummary, PMC7227117 full text, and the sample records of GSE127506/127507/137813/137814 all fetched live from NCBI 2026-09-23 and cached alongside the script; SRA runinfo fetched per experiment

     Oncofusion knowledge graph, coordinator · internal analysis, reproducible from the repository 2026
     used by Hunting the one reagent that would unbind every share-based result in this thread: the fly/human ratio is in no supplementary table and the words dm6 and scale factor appear zero times in the full text - and the 181116 batch the processing line names is in NONE of the 78 samples across all four subseries of GSE127508, so no deposited sample is established to carry the spike-in at all
247. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.trial_registry
     ClinicalTrials.gov registry query for CBFB-SMMHC / AI-10-49 interventional studies (API v2, query.term=CBFB-SMMHC and AI-10-49): no registered trial of any CBFbeta-SMMHC:RUNX1 interface inhibitor exists as of 2026-09-19.

     US National Library of Medicine · ClinicalTrials.gov 2026
     used by Hypothesis — the menin lesson generalises: every non-enzymatic fusion has an obligate partner interface that is more druggable than the fusion
248. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O00425 (IF2B3_HUMAN), human IGF2BP3, 579 aa

     · UniProt Consortium 2026
     used by Hypothesis: IGF2BP2 and IGF2BP3 buffer each other in KMT2A::AFF1 leukaemia, so single-gene CRISPR under-reports both, IGF2BP3 — an RNA-binding protein required for MLL-Af4 leukaemogenesis in mice that CRISPR barely touches in human lines
249. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 41307127
     A small molecule inhibitor of RNA-binding protein IGF2BP3 shows anti-leukemic activity

     Jaiswal AK, et al. · Haematologica 2026
     used by Hypothesis: IGF2BP2 and IGF2BP3 buffer each other in KMT2A::AFF1 leukaemia, so single-gene CRISPR under-reports both, I3IN-002 — the first small-molecule IGF2BP3 inhibitor with in vivo activity in an MLL-Af4 model, IGF2BP3 marks the fetal programme AND is required for B-ALL survival - the trap is not expression-for-requirement, it is requirement-for-state-maintenance, IGF2BP3 works in cytoplasmic RNA granules - the only compartment in this beat where a drug is already pointed, and nobody has looked at it in a leukaemia cell
250. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
     PubMed E-utilities counted-absence searches, run 2026-09-20: (MLL OR KMT2A) AND (loop anchor OR cohesin) AND breakpoint returns 0; (MLL OR KMT2A) AND breakpoint cluster region AND CTCF returns 0

     Q32-break-machinery · NCBI E-utilities 2026
     used by Hypothesis: KMT2A and AFF1 break where they do because both breakpoint regions are CTCF/cohesin loop anchors sitting in the same nuclear hub
251. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.paperPMID 41925057
     Successful Management of Lineage Switch Infant Leukemia With Revumenib and Hematopoietic Cell Transplantation.

     Granberg RE, Magee JA, Shenoy S, et al. · Pediatr Blood Cancer 2026
     used by Hypothesis: menin inhibition pushes cells toward the GMP-like state, and the GMP-like state is where menin inhibition works best — so a lineage switch on therapy should predict response, not failure, Lineage switch as a menin-inhibitor escape route — documented in a patient on revumenib, and invisible to every resistance-mutation screen
252. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.trial_registry
     ClinicalTrials.gov API v2 search across menin inhibitors, retrieved 2026-09-18

     US National Library of Medicine, ClinicalTrials.gov · ClinicalTrials.gov 2026
     used by Hypothesis: reserving menin inhibitors for relapse in infants is actively harmful, because pretreated disease is already resistant, Kura Oncology — ziftomenib (KO-539): an adults-only sponsor that quietly supplies infant trials
253. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.trial_registry
     TINI 2: Total Therapy for Infants With Acute Lymphoblastic Leukemia II

     Gruber TA (sponsor-investigator) · ClinicalTrials.gov 2026
     used by Hypothesis: reserving menin inhibitors for relapse in infants is actively harmful, because pretreated disease is already resistant, Kura Oncology — ziftomenib (KO-539): an adults-only sponsor that quietly supplies infant trials
254. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch and Open Targets Platform DepMap query, run 2026-09-20; full counts and name lists in ana-set-nup214-menin-bounded-absence

     · NCBI PubMed / Open Targets 2026
     used by Hypothesis: SET::NUP214 activates HOXA partly through recruited wild-type MLL1, which would make a KMT2A-unrearranged leukaemia menin-inhibitor-sensitive, Menin has never been tested against SET::NUP214 - a bounded absence in three independent registers: literature, cell-line dependency data, and the founding paper's own blots, SET::NUP214 is the second KMT2A-free HOXA fusion, and it converges on the same two proteins CALM-AF10 uses: CRM1 and DOT1L - and so does NPM1c, which IS menin-dependent (corrected 2026-09-21), Three addresses, one output: what SET::NUP214 actually does to the menin-interface hypothesis, and why it is a weaker test than CALM-AF10
255. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 42242459
     Inhibition of MLLT1 Limits Growth of KMT2A::AFF1 Leukemias Without Killing Healthy Hematopoietic Stem Cells.

     Rajhansa S, Crump NT, Khoo HM, Dopico-Fernandez A, Bozhilov Y, Brennan PE, Fedorov O, Adams C, Farnie G, Milne TA, Wilkinson AC · Experimental Hematology 2026
     used by Hypothesis: YEATS-pocket occupancy disables the reader module of all three SEC-family complexes in proportion to how much of the reader pool each holds — so the drug's footprint is set by an unmeasured partition, not by the fusion, Scored against the literature: the composition half of the YEATS-selectivity objection holds and the selectivity half is refuted — a scaffold-blind probe already has an in vivo window in the index fusion with no HSPC toxicity, SGC-iMLLT - the MLLT1/MLLT3 YEATS chemical probe, and the 2026 paper that put it into KMT2A::AFF1 in vivo with a healthy-HSPC comparison, The shared reader sits in a complex whose only well-defined normal job is parent-of-origin silencing — and the published safety package for YEATS inhibition is entirely haematopoietic, Two surfaces, two jobs: the AHD picks the scaffold and the YEATS pocket reads the histone — so a YEATS ligand cannot ask which of the three SEC-family complexes it is disabling
256. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
     computed 2026-09-23 from cBioPortal ccle_broad_2025 mutationType joined via DEPMAP_ID to DepMap Chronos (Open Targets GraphQL, dataVersion 26.06), with KMT2A-fusion status from Cellosaurus var:KMT2A AND dr:DepMap; method as in analyses/depmap-arid1b-truncating-stratum-redone/

     Oncofusion knowledge graph, coordinator · internal analysis, reproducible from the repository 2026
     used by I withheld these four numbers last cycle to keep an underpowered contrast out of a narrative, and they point the OTHER WAY: the four truncating-ARID1A leukaemia lines mean -0.0401 against a leukaemia wild-type of -0.0923, a naive +0.0523 where pan-cancer gives -0.2475. And NONE of the four carries a KMT2A fusion, so the intersection this whole thread needs is EMPTY, not merely small, Redone at 11x the power: at n=124 the truncating-ARID1A group IS materially lineage-concentrated (TVD permutation p = 0.00020, against p = 0.42 at n=11), so this time the lineage test had something real to remove - and the effect survives it at -0.2516. The missense null is tight, CI95 (-0.0242, +0.0473), excluding -0.10. And there are now 4 truncating-ARID1A leukaemia lines, one short of testable
257. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed E-utilities esearch record counts for ICE1 and KIAA0947 against KMT2A, MLL and leukaemia, run for this beat

     · NCBI PubMed, queried 2026-09-19 2026
     used by ICE1 — the 2,266-residue scaffold of the little elongation complex, the subunit that acts at initiation, and zero papers connecting it to leukaemia of any kind
258. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9Y2F5 (ICE1_HUMAN), Little elongation complex subunit 1

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by ICE1 — the 2,266-residue scaffold of the little elongation complex, the subunit that acts at initiation, and zero papers connecting it to leukaemia of any kind
259. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q659A1 (ICE2_HUMAN), Little elongation complex subunit 2

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by ICE2 — the fourth LEC subunit, the one with no assigned step, no structure, and no leukaemia literature
260. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed E-utilities esearch record counts for ICE2 and its aliases against KMT2A, MLL and leukaemia, run for this beat

     · NCBI PubMed, queried 2026-09-19 2026
     used by ICE2 — the fourth LEC subunit, the one with no assigned step, no structure, and no leukaemia literature
261. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P41134 (ID1_HUMAN) and HGNC REST fetch/symbol/ID1

     2026
     used by ID1 - the only OTHER named factor whose requirement for a KMT2A fusion depends on cell of origin: needed in fetal-liver-derived MLL-AF9 leukaemia, actively restraining in bone-marrow-derived
262. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI E-utilities esearch against PubMed, run via scripts/pubmed_safe.py

     2026
     used by ID1 - the only OTHER named factor whose requirement for a KMT2A fusion depends on cell of origin: needed in fetal-liver-derived MLL-AF9 leukaemia, actively restraining in bone-marrow-derived
263. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     Independent Fisher exact and Wilson-interval recomputation of the KMT2A-altered versus KMT2A-wild-type co-mutation table of PMID 41514668

     Oncofusion knowledge-graph project, Q81-methylome-axis · Recomputed 2026-09-21 from percentages read out of PMC12784994 Table 2; counts back-calculated as round(pct x n), accurate to about one case 2026
     used by IDH1 - the same oncometabolite, the same assay, and NO enrichment in KMT2A-rearranged AML (6.7% vs 7.6%, p = 0.53): the control that makes the IDH2 result interpretable, IDH2 - the hypermethylating co-mutation that IS enriched in KMT2A-rearranged AML (16.0% vs 10.4%), at p = 0.0004 and not the p < 0.0001 the abstract claims, The methylome co-mutation table, recomputed: IDH2 up at p = 0.0004 and not p < 0.0001, IDH1 and DNMT3A flat, and the abstract disagrees with its own Table 2
264. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O75874 (IDHC_HUMAN), Isocitrate dehydrogenase [NADP] cytoplasmic

     UniProt Consortium · UniProtKB 2026
     used by IDH1 - the same oncometabolite, the same assay, and NO enrichment in KMT2A-rearranged AML (6.7% vs 7.6%, p = 0.53): the control that makes the IDH2 result interpretable
265. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed human entry P15260 (INGR1_HUMAN)

     UniProt Consortium · UniProtKB 2026
     used by IFNGR1 - the receptor the whole antigen-presentation mechanism runs through, and the one where low-dose interferon-gamma makes MLL-fusion leukaemia worse
266. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42380666
     Lineage-restricted dependency on an oncofetal SNHG29-IGF2BP1 RNA axis in acute megakaryoblastic leukemia

     Winkler R, et al. · Leukemia 2026
     used by IGF2BP1 — the IMP paralogue that belongs to a DIFFERENT fusion, and the cleanest control the family offers
267. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9NZI8 (IF2B1_HUMAN), human IGF2BP1, 577 aa

     · UniProt Consortium 2026
     used by IGF2BP1 — the IMP paralogue that belongs to a DIFFERENT fusion, and the cleanest control the family offers
268. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9Y6M1 (IF2B2_HUMAN), human IGF2BP2, 599 aa

     · UniProt Consortium 2026
     used by IGF2BP2 — the paralogue co-over-expressed with IGF2BP3 in MLL/AF4 B-ALL, and the one with an inhibitor in another leukaemia
269. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9Y6M1 (IF2B2_HUMAN), SUBCELLULAR LOCATION comment with all four values, their evidence arrays and the note, plus TISSUE SPECIFICITY, fetched live 2026-09-21

     UniProt Consortium · Databases 2026
     used by IGF2BP2 — the paralogue co-over-expressed with IGF2BP3 in MLL/AF4 B-ALL, and the one with an inhibitor in another leukaemia
270. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O00425 (IF2B3_HUMAN) - subcellular location with evidence codes, fetched 2026-09-20

     UniProt Consortium · UniProtKB 2026
     used by IGF2BP3 works in cytoplasmic RNA granules - the only compartment in this beat where a drug is already pointed, and nobody has looked at it in a leukaemia cell
271. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     Q147 pre-registration - FLOOR-B and the decision not to use IgG as the gate

     Iqbal Lab oncofusion knowledge graph, beat Q147 · this project 2026
     used by IgG passes this project's occupancy gate at TWICE the rate of the fusion antibody - because the gate is normalised to each library's own promoter mean and IgG has almost none
272. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry O14920 (IKKB_HUMAN), Inhibitor of nuclear factor kappa-B kinase subunit beta

     UniProt Consortium · UniProt 2026
     used by IKBKB (IKK-beta) — the kinase whose knockdown tracks MLL-leukaemia growth most tightly, and whose inhibitors have failed clinically for a reason
273. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch, db=pubmed, run 2026-09-20

     NCBI · PubMed 2026
     used by IKBKB (IKK-beta) — the kinase whose knockdown tracks MLL-leukaemia growth most tightly, and whose inhibitors have failed clinically for a reason
274. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch, db=pubmed, run 2026-09-20

     NCBI · PubMed 2026
     used by IKBKG (NEMO) — the scaffold that makes the canonical complex a complex, and a symbol that returns ZERO records in this disease
275. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q9Y6K9 (NEMO_HUMAN), NF-kappa-B essential modulator

     UniProt Consortium · UniProt 2026
     used by IKBKG (NEMO) — the scaffold that makes the canonical complex a complex, and a symbol that returns ZERO records in this disease
276. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch, db=pubmed, run 2026-09-20

     NCBI · PubMed 2026
     used by IKK/NF-kB retains MLL on chromatin — BOTH the fusion and wild-type MLL, at two promoters, in mouse myeloid AML, and it is occupancy loss rather than protein loss, The NF-kB story in KMT2A-rearranged leukaemia is a myeloid story, and the lymphoid half is not a weaker version of it — it is a different subject
277. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed human entry Q13422 (IKZF1_HUMAN), retrieved by gene_exact:IKZF1 with fields accession, gene_primary, gene_synonym, protein_name, length and the zinc-finger feature table

     UniProt Consortium · UniProt 2026
     used by IKZF1 - the defining co-lesion of every other high-risk B-ALL, and this disease does not use it until after treatment
278. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 41419607
     Targeting IL-1/IRAK1/4 signaling in acute myeloid leukemia stem cells following treatment and relapse.

     Ho TC, LaMere MW, ... Becker MW · Leukemia 2026
     used by IL-1/IRAK1/4 — the receptor-proximal input the MLL screen actually pointed at, with an Il1r1 knockout in MLL-AF9 mice and an inhibitor that spares normal stem cells
279. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch, db=pubmed, run 2026-09-20

     NCBI · PubMed 2026
     used by IL-1/IRAK1/4 — the receptor-proximal input the MLL screen actually pointed at, with an Il1r1 knockout in MLL-AF9 mice and an inhibitor that spares normal stem cells
280. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P26951 (IL3RA_HUMAN), Interleukin-3 receptor subunit alpha, 378 aa, single reviewed human record, primary gene name IL3RA

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by IL3RA / CD123 - not just a myeloid target: the quartile of CD123 expression that carries the KMT2A rearrangements is the quartile that dies
281. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q12906 (ILF3_HUMAN) features, comments, PTMs and subcellular-location evidence codes; HGNC:6038 prev_symbol and alias_symbol via rest.genenames.org; retrieved 2026-09-22

     · UniProt Consortium / HGNC 2026
     used by ILF3 / NF90 - a nucleolar dsRNA-binding coactivator whose chromatin residency was mapped in the same leukaemia line that proximity-labelled KMT2A
282. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     IntAct REST findInteractions/Q12906 (987 indexed interactions), filtered to Q03164/O00255/O75475/Q9UHB7/Q8TEK3/P51825/Q03111/P42568/P55199/P55197 with experimentalRole, detectionMethod and hostOrganism read per row; retrieved 2026-09-22

     · IntAct molecular interaction database (EMBL-EBI) 2026
     used by ILF3 / NF90 - a nucleolar dsRNA-binding coactivator whose chromatin residency was mapped in the same leukaemia line that proximity-labelled KMT2A
283. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     analyses/depmap-kmt2a-selective-scan-full/results.json - 17,728 protein-coding genes, 11 Cellosaurus-annotated KMT2A-rearranged versus 43 other leukaemia lines, computed 2026-09-19

     · DepMap (Broad Institute), via this repository's scan 2026
     used by ILF3 / NF90 - a nucleolar dsRNA-binding coactivator whose chromatin residency was mapped in the same leukaemia line that proximity-labelled KMT2A
284. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI E-utilities esearch, db=pubmed, querytranslation read back from every response, with PubMed publication types read from efetch for PMID 34141456; run 2026-09-22

     · NCBI PubMed 2026
     used by ILF3 / NF90 - a nucleolar dsRNA-binding coactivator whose chromatin residency was mapped in the same leukaemia line that proximity-labelled KMT2A
285. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed esearch, three stated queries run 2026-09-19; counts 0, 0 and 1, the single record being a patient-cohort study

     · NCBI E-utilities 2026
     used by Immunoprecipitate the KMT2A fusion and map its phosphosites - the experiment this whole field has never done
286. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P12268 (IMDH2_HUMAN), Inosine-5-prime-monophosphate dehydrogenase 2

     UniProt Consortium · UniProt 2026
     used by IMPDH2 - the rate-limiting guanine-nucleotide enzyme whose inhibition lowers LEDGF and menin protein and dismantles the MLL-fusion complex itself
287. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
     analyses/q205-program-loop-simulation/program_loop.py and results.json, run 2026-10-14 (3,000 Latin-hypercube samples, seed 7)

     · this repository 2026
     used by In a competitive menin-binding scaffold with assumed rates, the drug exposure needed scales with menin relative to the fusion-menin Kd, and whether recovery after a lapse lags collapse is governed by the drug's residence time - a conditional counter-lead to the pulsed-dosing premise, not a prediction
288. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     IntAct PSICQUIC, MITAB2.7 rows for Q03164, O00255, O75475, Q9UHB7 and P51825, filtered on the twelve read-queue accessions

     · EMBL-EBI IntAct 2026
     used by In all 24 read-queue rows inspected, the candidate is the BAIT and this project's protein is the prey - nobody has ever tagged KMT2A, AFF4, menin or PSIP1 and found any of them; plus seven bounded rejections, PES1 / pescadillo (O00541) - the missing PeBoW subunit of this graph's nucleolar block, pan-essential in 96.9% of DepMap lines, and the one myeloid experiment on it shows proliferation WITHOUT a differentiation block, RSBN1 / KDM9 (Q5VWQ0) - an H4K20me2/me3 demethylase in the AFF4 proximity record, and the only read-queue partner that is a chromatin enzyme at all, The interactome coverage figure is computed on 651 of the 1,015 IntAct rows available - 64% - and the gap is worst for menin and LEDGF, the two baits the menin-interface hypothesis rests on
289. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     UniProt REST, gene_exact queries in reviewed human records for FGF12, PLCD3, DENND2D, FAM9A, MDK, ARRB2 and RPS11 with subcellular-location and function comments

     · UniProt Knowledgebase 2026
     used by In all 24 read-queue rows inspected, the candidate is the BAIT and this project's protein is the prey - nobody has ever tagged KMT2A, AFF4, menin or PSIP1 and found any of them; plus seven bounded rejections
290. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     UCSC Genome Browser API, hg19 cpgIslandExt track - 30,344 islands, 27,537 on chr1-22 and chrX, fetched 2026-09-23

     · UCSC Genome Browser 2026
     used by In human RS4;11 (KMT2A::AFF1), menin occupancy at its own top 0.1% of 2 kb bins falls 14.9x to 2.0x over the track median and its share of total coverage falls to 0.200 - reproducing Q117's murine FLAG-MLLAF9 figures (15.9x to 3.0x, ratio 0.179) to within 1.3-fold on all five statistics, Q117's CpG-island falsifier reproduces in the human index fusion almost to the decimal - gained bins 5.66% on an island against a class-matched null of 4.23%, fold 1.34, Fisher p = 0.49, where Q117 got fold 1.35 and p = 0.53 - so the CXXC-redistribution model fails in human RS4;11 as it did in mouse
291. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Bounded PubMed absence for alternative lengthening of telomeres in KMT2A-rearranged and lymphoblastic leukaemia, run through scripts/pubmed_safe.py

     · PubMed (NCBI E-utilities), via this project's pubmed_safe wrapper 2026
     used by In pancreatic neuroendocrine tumours MEN1 and DAXX/ATRX are the two commonest mutations of the same tumour - and both are LOST there while leukaemia needs both intact
292. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.analysis
     analyses/arid1a-kmt2a-cooccurrence-in-patients/run.py and results.json, this repository; cBioPortal studies aml_stjude_2024 and all_phase2_target_2018_pub, queried 2026-09-23; KMT2A entrez 4297 verified against /api/genes before use

     Oncofusion knowledge graph, coordinator · internal analysis, reproducible from the repository 2026
     used by In St. Jude paediatric AML, 2 of the 6 ARID1A-mutant cases are KMT2A-rearranged and BOTH ARID1A mutations are TRUNCATING frameshifts in KMT2A::MLLT10 cases - so the exact combination cycle 86 showed the ARID1B dependency is confined to DOES occur in patients, and cycle 88's empty DepMap intersection is a cell-line sampling artefact rather than a fact about the disease. The paediatric ALL cohort returned zero ARID1A mutations, which is panel coverage and not biology
293. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     Q154 label permutation over the published GSE252378 oncoprotein-target call table

     Iqbal Lab oncofusion knowledge graph, beat Q154 · this project 2026
     used by In the deposit paper's own target-gene table, the AFF1-exclusive class is 64 genes against a permutation null of 2.3, and it survives call-rate matching, institution stratification, B-lineage restriction and patient collapse, IRX1's own three-sample pattern is p = 0.022 naively and 0.077-0.176 once patients, institution or lineage are held fixed - the class it belongs to is significant, IRX1 alone is not, KMT2A-N/C CUT&RUN on one untreated KMT2A::AFF1 blast from outside Texas Children's, scored at the six AFF1-exclusive gene bodies with a pre-declared margin column
294. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     Q154 pre-registration, written before computation

     Iqbal Lab oncofusion knowledge graph, beat Q154 · this project 2026
     used by In the deposit paper's own target-gene table, the AFF1-exclusive class is 64 genes against a permutation null of 2.3, and it survives call-rate matching, institution stratification, B-lineage restriction and patient collapse, IRX1's own three-sample pattern is p = 0.022 naively and 0.077-0.176 once patients, institution or lineage are held fixed - the class it belongs to is significant, IRX1 alone is not
295. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 40898981
     Off-the-shelf dual CAR-iNKT cell immunotherapy eradicates medullary and leptomeningeal high-risk KMT2A-rearranged leukemia.

     Ren H, Elliott N, Lye B, Sharif Shohan MU, Cross JW, Field L, et al. · Blood 2026
     used by In this fusion family, MHC class I is not silenced - it is elevated and load-bearing, holding NK cells off the leukaemia stem cell, The CNS-adapted state — leukaemia-propagating cells reprogrammed by the central nervous system niche, and worse at restarting systemic disease afterwards, The NK cell - the effector arm of haploidentical transplant, the one this disease is documented to evade, and the cell CLEC12A was named on, Thomas Milne (MRC WIMM, Oxford) — MLL-AF4 target biology, enhancer architecture and PROM1/CD133
296. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
     analyses/what-this-corpus-actually-cites/add_abstracts.py and abstract-coverage.json, this repository, computed 2026-09-24 with abstracts fetched live from PubMed efetch in batches of 180

     Oncofusion knowledge graph, coordinator · internal analysis, reproducible from the repository 2026
     used by Indexing abstracts for all 4,000 cited papers, the U2 that has bound the citation index since it was built - 98.9% retrieved, and across seven probe topics abstract search reaches 144 papers title search cannot see, including 54 single-cell papers and 25 CRISPR screens
297. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
     analyses/what-deposits-this-corpus-actually-cites/run.py, results.json and deposit-index.json, this repository, computed 2026-09-24 against the committed node files with series records fetched live from the GEO accession endpoint

     Oncofusion knowledge graph, coordinator · internal analysis, reproducible from the repository 2026
     used by Indexing every deposit this corpus cites - 504 accessions, 102 GEO series, all 102 resolving - because the citation index repaired last cycle indexes papers only, and half the known absence failures were refuted by a dataset rather than by a paper
298. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
     analyses/what-this-corpus-actually-cites/run.py, results.json and citation-index.json, this repository, computed 2026-09-23 against the committed node files with titles fetched live from PubMed esummary

     Oncofusion knowledge graph, coordinator · internal analysis, reproducible from the repository 2026
     used by Indexing every PMID in every entry - CORRECTED to 4,000 distinct papers across 2,411 entries after the original regex was found to miss 73.7% of them by matching prose but not the schema's own citation field, an undercount that made this entry declare a gap the corpus refuted 14 times over, The citation index built to stop false gap claims made one: its regex matched prose but not the schema's own pmid field, missing 73.7% of the corpus's citations, and the single-cell gap it selected was refuted by a paper already cited in fourteen entries
299. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9H160 (ING2_HUMAN), Inhibitor of growth protein 2 - FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, DOMAIN, feature table and cross-references, fetched 2026-09-22

     · UniProt Consortium 2026
     used by ING2 - the PHD finger that reads H3K4me3 and turns it into REPRESSION, and whose founding co-crystal is filed under the MOUSE accession
300. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9H160 cross-references; RCSB Search API accession query on Q9H160 (HTTP 204); RCSB Data API entries 2G6Q, 9M4S and 1WES with polymer-entity SIFTS reference_sequence_identifiers; UniProtKB Q9ESK4 and B3H615 organism readback - all fetched 2026-09-22

     · RCSB PDB and UniProt 2026
     used by ING2 - the PHD finger that reads H3K4me3 and turns it into REPRESSION, and whose founding co-crystal is filed under the MOUSE accession
301. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset
     NCBI GEO GSM8123359 (MLLAF9 Control - DMSO FLAG) annotated against UCSC mm10 refGene via api.genome.ucsc.edu, 2026-09-23

     · NCBI Gene Expression Omnibus / UCSC Genome Browser 2026
     used by Instrument check before any conclusion: reading a browser-track .tdf with a hand-written binner and ranking the result blind returns the Hoxa cluster in five of the top twenty bins, plus Meis1, Jmjd1c, Six1, Arid2, Ncor1 and Tsc22d2 - the canonical MLL-AF9 programme, which is what the track claims to be
302. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UCSC Genome Browser API, list/chromosomes for mm10 and mm39, fetched 2026-09-23

     · UCSC Genome Browser 2026
     used by Instrument check before any conclusion: reading a browser-track .tdf with a hand-written binner and ranking the result blind returns the Hoxa cluster in five of the top twenty bins, plus Meis1, Jmjd1c, Six1, Arid2, Ncor1 and Tsc22d2 - the canonical MLL-AF9 programme, which is what the track claims to be
303. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     IntAct REST findInteractor (mll_af9, mll_enl, mll_aff4_fusion, EBI-2620048, EBI-2620075) and findInteractions for each accession, with interactorXrefs, interactorPreferredIdentifier, interactionCount, experimentalRole, detectionMethod, hostOrganism and publicationPubmedIdentifier read per record; retrieved 2026-09-22

     · IntAct molecular interaction database (EMBL-EBI) 2026
     used by IntAct curates 47 interactions against engineered MLL fusion proteins, and every accession-keyed query in this project is blind to all of them - while its PSICQUIC mirror stops at 2024, MED19 - the Mediator subunit curated against an engineered MLL-AFF4 fusion protein, and the one REST uses to deliver G9a, The federated sweep this graph prescribes for the missing index-fusion interactor cannot be run: PSICQUIC free text returns ZERO for `mll_af9`, an entity that provably exists and returns 32 records under its accession - so every provider's zero in that sweep is uninterpretable
304. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     analyses/core-complex-interactome-gap/run.py - gene_of() regex on the MITAB alias field, PSICQUIC search/query/<accession>?format=tab25 endpoint; and the returned MITAB rows for query/Q03164 and query/Q9UHB7 showing interaction EBI-4321349 with alias field psi-mi:mll_aff4_fusion(display_short)|psi-mi:EBI-2620048(display_long); read and executed 2026-09-22

     · This repository / IntAct PSICQUIC (EMBL-EBI) 2026
     used by IntAct curates 47 interactions against engineered MLL fusion proteins, and every accession-keyed query in this project is blind to all of them - while its PSICQUIC mirror stops at 2024
305. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     IntAct PSICQUIC search/query/Q9UHB7 and /P48426 (format=tab25, maxResults=4000), all pubmed identifiers extracted per row, compared against IntAct REST findInteractions for the same accessions; run 2026-09-22

     · IntAct molecular interaction database (EMBL-EBI) 2026
     used by IntAct curates 47 interactions against engineered MLL fusion proteins, and every accession-keyed query in this project is blind to all of them - while its PSICQUIC mirror stops at 2024
306. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     IntAct REST ws/interaction/findInteractions free-text query controls for MLL fusion-entity labels, run 2026-09-21

     · EMBL-EBI IntAct 2026
     used by IntAct curates SEVEN MLL fusion proteins as first-class interactors - ENL, AFF4, AF9, GAS7, ELL, AF6 and CALM - and not the index one
307. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     IntAct REST ws/interaction/findInteractions free-text sweep over the queries mll, KMT2A, AFF1, MLL-AF4 and fusion, non-UniProt and fusion-labelled interactors enumerated, run 2026-09-21

     · EMBL-EBI IntAct 2026
     used by IntAct curates SEVEN MLL fusion proteins as first-class interactors - ENL, AFF4, AF9, GAS7, ELL, AF6 and CALM - and not the index one
308. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch record counts for 41 candidate interactor queries against KMT2A, MLL and MLL-fusion terms, run for interactome round 4

     · NCBI PubMed, queried 2026-09-19 2026
     used by Interactome round 4: what was counted, what was written, what was rejected, and the two alias traps this beat fell into and caught
309. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch comparison of alias-inflated and corrected queries for NELFE and EAF2, run for interactome round 4

     · NCBI PubMed, queried 2026-09-19 2026
     used by Interactome round 4: what was counted, what was written, what was rejected, and the two alias traps this beat fell into and caught
310. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch record counts for 42 candidate queries across FACT, NSL, MSL, the COMPASS remainder and Mediator, run for interactome round 5

     · NCBI PubMed, queried 2026-09-19 2026
     used by Interactome round 5: 42 queries, 13 entries written, 9 candidates rejected with counts, and four alias failures of four different kinds, Lineage-split dependency for the round 5 panel: 23 genes, 2 myeloid-identity artefacts caught, and 3 survivors of which one has no literature at all, NSL complex - the MOF assembly that five NUP98 fusions bind alongside MLL1, and that competes with MLL/COMPASS for WDR5
311. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q7Z3B3 (KANL1_HUMAN), KAT8 regulatory NSL complex subunit 1

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by Interactome round 5: 42 queries, 13 entries written, 9 candidates rejected with counts, and four alias failures of four different kinds, KANSL1 - the NSL scaffold, and the protein through which WDR5 binding to NSL and to MLL/COMPASS is mutually exclusive
312. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB search gene_exact:MED1 AND organism_id:9606 AND reviewed:true - returns Q15648 (MED1) and O95243 (MBD4, which lists MED1 as a synonym)

     · UniProt Knowledgebase, reviewed (Swiss-Prot), queried 2026-09-19 2026
     used by Interactome round 5: 42 queries, 13 entries written, 9 candidates rejected with counts, and four alias failures of four different kinds
313. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.trial_registry
     Interfant-21 International Collaborative Treatment Protocol for Infants Under One Year With KMT2A-rearranged Acute Lymphoblastic Leukemia or Mixed Phenotype Acute Leukemia

     Princess Maxima Center for Pediatric Oncology · ClinicalTrials.gov 2026
     used by Interfant-21 (NCT05327894) — the randomised test of blinatumomab in infant KMT2A-rearranged ALL, open now
314. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.trial_registry
     A Phase 2 Study of Blinatumomab in Combination With Chemotherapy for Infants With Newly Diagnosed Acute Lymphoblastic Leukemia With Randomization of KMT2A-Rearranged Patients to Addition of Venetoclax

     National Cancer Institute (NCI) · ClinicalTrials.gov 2026
     used by Interfant-21 (NCT05327894) — the randomised test of blinatumomab in infant KMT2A-rearranged ALL, open now, Venetoclax in KMT2A-rearranged leukemia — the apoptotic partner every other drug needs
315. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     ana-q147-irx1-fusion-occupancy-is-confined-to-kmt2a-aff1 and absence-q149-... (this graph)

     Iqbal Lab oncofusion knowledge graph, beat Q152 · this project 2026
     used by IRX1 sits in the 2-of-8 tier - two different patients, not the same one twice - and is not in the recurrent core
316. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     Q154 IRX1/IRX2 cross-instrument occupancy table (gene body, promoter by fragment midpoints, promoter by bigWig)

     Iqbal Lab oncofusion knowledge graph, beat Q154 · this project 2026
     used by IRX2 IS fusion-occupied at gene-body scale in p454 - and q151's promoter-scale zero of 27 turns on one replicate 5% below the threshold, which two other instruments put above it
317. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     q151 null for the q147 occupancy rule at promoter scale, over 19,404 refGene promoters x 27 samples

     Iqbal Lab oncofusion knowledge graph, beat Q151 · this project 2026
     used by IRX2 is not fusion-occupied at promoter scale in GSE252378: 0 of 27 samples, against a null of 2.73, The 2.03-fold over-representation of shared windows among fusion-occupied promoters is generic promoter activity, not a fusion preference - and if it is not, the rule is finding something different from what it claims, The occupancy rule this project has used since q145 calls a tenth of ALL promoters occupied, and no entry using it records that
318. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
     q151 threshold sensitivity sweep and near-miss decomposition, GSE252378

     Iqbal Lab oncofusion knowledge graph, beat Q151 · this project 2026
     used by IRX2 is not fusion-occupied at promoter scale in GSE252378: 0 of 27 samples, against a null of 2.73, IRX2-DT (C5orf38) - the divergent partner 215 bp from the IRX2 TSS that makes every 2 kb IRX2 window ambiguous
319. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     IRX2-DT IRX2 divergent transcript [Homo sapiens (human)], Gene ID 153571

     NCBI Gene · NCBI Gene 2026
     used by IRX2-DT (C5orf38) - the divergent partner 215 bp from the IRX2 TSS that makes every 2 kb IRX2 window ambiguous
320. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UCSC Genome Browser hg38 refGene track, chr5:2,745,000-2,760,000

     UCSC Genome Browser, api.genome.ucsc.edu · UCSC Genome Browser 2026
     used by IRX2-DT (C5orf38) - the divergent partner 215 bp from the IRX2 TSS that makes every 2 kb IRX2 window ambiguous
321. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q969H0, subcellular location and tissue specificity, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by Is menin an SCF-FBXW7 substrate? A one-week immunoblot and a free desk scan that settle Arm A, MEN1-FBXW7 is four alleles of ONE BRET assay, all typed 'mutation with no effect' - declined, and it is the most insidious class, Three of menin's nine declined partners are E3 ligase substrate receptors - either menin turnover is ubiquitin-controlled, or substrate receptors are this beat's artefact signature
322. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch counts for KMT2A/MAML2/menin intersection queries, run 2026-09-19

     National Center for Biotechnology Information (NCBI), PubMed · PubMed (NCBI E-utilities) 2026
     used by Is the menin interface a property of the fusion or of the blood? Test KMT2A::MAML2 thymoma, KMT2A::MAML2 type B2/B3 thymoma - the same fusion, a different organ, a different disease
323. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UCSC Genome Browser REST API, hg38 ncbiRefSeqSelect track, NM_005934.4 (MLLT1) and NM_004529.4 (MLLT3)

     · UCSC Genome Browser 2026
     used by Is the YEATS asymmetry just intron geometry? Computed from hg38: the direction is explained, the magnitude is not, and both genes fail the same prediction, The 2x2 paralogue swap: separate 'is the reader there' from 'which backbone is it on', in one background with matched expression, The transfer rule: which MLL-AF9 results can be carried into t(11;19) and t(4;11), and which are statements about a protein missing a reading module, The YEATS asymmetry is breakage geography, not selection: the reader's fate is decided by where topoisomerase II cuts, before any leukaemia exists
324. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P13612 (ITA4_HUMAN)

     · UniProtKB 2026
     used by ITGA4 (CD49d, the alpha-4 of VLA-4) - the niche adhesion subunit with an approved antibody and a 2026 KMT2A-r B-ALL xenograft result
325. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     ChEMBL molecule record CHEMBL3989958 (IVOSIDENIB)

     ChEMBL, EMBL-EBI · ChEMBL database 2026
     used by Ivosidenib - the approved IDH1 inhibitor, recorded here so that nobody reaches for it: IDH1 is the paralogue that is NOT enriched in KMT2A-rearranged AML
326. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 42431943
     Distinct roles of the JADE and BRPF scaffolding subunits of the acetyltransferase HBO1 complex.

     Gaurav N, Ebert LK, Lachance C, Selvam K, Chen RW, et al. · Nat Commun 2026
     used by JADE3 / PHF16 (Q92613) - the HBO1-complex scaffold with the strongest pan-fusion evidence in this beat, and an independent published contact with MLL
327. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed human entry P23458 (JAK1_HUMAN)

     UniProt Consortium · UniProtKB 2026
     used by JAK1 - recruited and stabilised by AF10 fusions, and the kinase whose downstream STAT1 the class I effect of menin inhibition explicitly does not need
328. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P23458 (JAK1_HUMAN), SUBCELLULAR LOCATION comment with its evidence array read back field by field, fetched live 2026-09-21

     UniProt Consortium · Databases 2026
     used by JAK1 - recruited and stabilised by AF10 fusions, and the kinase whose downstream STAT1 the class I effect of menin inhibition explicitly does not need
329. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q86VZ6 (JAZF1_HUMAN): reviewed record, length, gene names and subcellular-location comment

     UniProt Consortium · UniProtKB/Swiss-Prot 2026
     used by JAZF1 - a 243-residue zinc-finger protein that turned out to be a NuA4 subunit, and the 5' donor of the commonest endometrial-stromal-sarcoma fusion
330. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     HGNC record for JAZF1 (HGNC:28917)

     HUGO Gene Nomenclature Committee · HGNC REST 2026
     used by JAZF1 - a 243-residue zinc-finger protein that turned out to be a NuA4 subunit, and the 5' donor of the commonest endometrial-stromal-sarcoma fusion
331. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q15652 (JHD2C_HUMAN, 2,540 aa) FUNCTION and SUBUNIT comments; resolved by gene_exact:JMJD1C and gene_exact:KDM3C both returning the same single reviewed human row, with the primary gene name and length read back

     · UniProt Consortium 2026
     used by JDI-12 - published as a JMJD1C inhibitor that preferentially kills KMT2A-rearranged leukaemia and spares cord blood, then used as 'KDM3i' to CREATE KMT2A rearrangements in cord-blood progenitors, by two papers that do not cite each other, JMJD1C / KDM3C - named in three entries of this graph as one of the only loci that loses fusion occupancy under a menin inhibitor, ranked 23rd of 17,728 for KMT2A-selective dependency in this project's own scan, with the strongest published shRNA effect in SEM - and no entry until now
332. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
     IntAct molecular interaction database, PSICQUIC MITAB 2.7, query id:Q8N9B5 AND id:Q9UHB7, 1 row retrieved 2026-09-21

     · IntAct (EMBL-EBI) 2026
     used by JMY - one AP-MS row with AFF4, in HCT116 only, from a paper whose whole argument is that interactomes differ between cell lines
333. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q8N9B5 (JMY_HUMAN, Junction-mediating and -regulatory protein), subcellular location and function comments with evidence codes

     · UniProtKB/Swiss-Prot 2026
     used by JMY - one AP-MS row with AFF4, in HCT116 only, from a paper whose whole argument is that interactomes differ between cell lines
334. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted-absence search for JMY against MLL, KMT2A and leukaemia, run 2026-09-21

     · PubMed (NCBI) 2026
     used by JMY - one AP-MS row with AFF4, in HCT116 only, from a paper whose whole argument is that interactomes differ between cell lines
335. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.trial_registry
     ClinicalTrials.gov registry records for NCT05453903, NCT06852222, NCT03013998 and NCT07223814, retrieved via the ClinicalTrials.gov API v2 intervention search on bleximenib / JNJ-75276617

     Janssen Research & Development, LLC; Beat AML, LLC; Stichting Hemato-Oncologie voor Volwassenen Nederland (HOVON) · ClinicalTrials.gov 2026
     used by Johnson & Johnson / Janssen — bleximenib (JNJ-75276617): paediatric from age 2, but not infants, and the dedicated child study was withdrawn
336. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.trial_registry
     A Phase I/Ib Study of JNJ-75276617 in Combination With Conventional Chemotherapy for Pediatric and Young Adult Participants With Relapsed/Refractory Acute Leukemias Harboring KMT2A, NPM1, or Nucleoporin Gene Alterations

     Janssen Research & Development, LLC · ClinicalTrials.gov 2026
     used by Johnson & Johnson / Janssen — bleximenib (JNJ-75276617): paediatric from age 2, but not infants, and the dedicated child study was withdrawn, The counter-argument: the menin field is an adult field, and the infant studies were withdrawn
337. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P17535 (JUND_HUMAN), Transcription factor JunD

     UniProt Consortium · UniProtKB/Swiss-Prot 2026
     used by JUND - the AP-1 subunit menin holds down, and the one a menin inhibitor lets go
338. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed E-utilities esearch record counts for the NSL complex subunits against KMT2A, MLL and leukaemia, run for interactome round 5

     · NCBI PubMed, queried 2026-09-19 2026
     used by KANSL1 - the NSL scaffold, and the protein through which WDR5 binding to NSL and to MLL/COMPASS is mutually exclusive
339. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 41680331
     Integrative transcriptomics and electrophysiological profiling of hiPSC-derived neurons identifies novel druggable pathways in Koolen-de Vries Syndrome.

     Verboven AHA, Puvogel S, Latour BL, Kolsters N, Lewerissa EI, Mijdam R, Dyke E, Duineveld D, Zoodsma M, Claassen WJJ, Oudakker A, Schoenmaker C, Koolen DA, de Vries BBA, 't Hoen PAC, Linda K, Nadif Kasri N · Mol Psychiatry 2026
     used by KANSL1 - the NSL scaffold, and the protein through which WDR5 binding to NSL and to MLL/COMPASS is mutually exclusive, Neuron - the off-target cell type that defines what KANSL1 loss costs a human being
340. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed E-utilities esearch record counts for the NSL complex subunits against KMT2A, MLL and leukaemia, run for interactome round 5

     · NCBI PubMed, queried 2026-09-19 2026
     used by KANSL2 - the second NSL subunit in the WDR5 structure, with one leukaemia record and a dependency profile that is the mirror image of a selective target
341. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9H9L4 (KANL2_HUMAN), KAT8 regulatory NSL complex subunit 2

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by KANSL2 - the second NSL subunit in the WDR5 structure, with one leukaemia record and a dependency profile that is the mirror image of a selective target
342. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q92830 (KAT2A_HUMAN), Histone acetyltransferase KAT2A

     UniProt Consortium · UniProtKB, retrieved 2026-09-20 2026
     used by KAT2A / GCN5 - the SAGA catalytic subunit that reaches this disease through its complex rather than through its own symbol, and whose only chemical tool degrades its paralogue too
343. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch: (MLL[tiab] OR KMT2A[tiab]) AND (KAT2A[tiab] OR GCN5[tiab]), run 2026-09-20, count 7, all seven title-checked by efetch

     NCBI E-utilities · PubMed 2026
     used by KAT2A / GCN5 - the SAGA catalytic subunit that reaches this disease through its complex rather than through its own symbol, and whose only chemical tool degrades its paralogue too
344. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch: (MLL[tiab] OR KMT2A[tiab]) AND SAGA[tiab], run 2026-09-20, count 3, all three title-checked by efetch (42523331, 42418681, 23894581)

     NCBI E-utilities · PubMed 2026
     used by KAT2A / GCN5 - the SAGA catalytic subunit that reaches this disease through its complex rather than through its own symbol, and whose only chemical tool degrades its paralogue too
345. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q92830 (KAT2A_HUMAN), SUBCELLULAR LOCATION comment with all evidence codes, sources and the free-text note, plus TISSUE SPECIFICITY, fetched live 2026-09-21

     UniProt Consortium · Databases 2026
     used by KAT2A / GCN5 - the SAGA catalytic subunit that reaches this disease through its complex rather than through its own symbol, and whose only chemical tool degrades its paralogue too
346. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q92831 (KAT2B_HUMAN), Histone acetyltransferase KAT2B

     UniProt Consortium · UniProtKB, retrieved 2026-09-20 2026
     used by KAT2B / PCAF - named in an existing entry's own id and never written, and the only acetyltransferase in this graph whose substrate is a fusion partner protein
347. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q92831 (KAT2B_HUMAN) - SUBCELLULAR LOCATION comment block with evidence codes

     · UniProt Consortium 2026
     used by KAT2B / PCAF - named in an existing entry's own id and never written, and the only acetyltransferase in this graph whose substrate is a fusion partner protein
348. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch: (MLL[tiab] OR KMT2A[tiab]) AND (KAT5[tiab] OR Tip60[tiab] OR HTATIP[tiab]), run 2026-09-20, count 7, all seven title-checked by efetch

     NCBI E-utilities · PubMed 2026
     used by KAT5 / Tip60 - the acetyltransferase in the only direct KMT2A-fusion histone-variant result, and both fusions tested were myeloid
349. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q92993 (KAT5_HUMAN), Histone acetyltransferase KAT5

     UniProt Consortium · UniProtKB, retrieved 2026-09-20 2026
     used by KAT5 / Tip60 - the acetyltransferase in the only direct KMT2A-fusion histone-variant result, and both fusions tested were myeloid
350. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     RCSB PDB entries 5GK9, 6MAJ, 6MAK, 7D0O, 7D0P, 7D0Q, 7D0R and 7D0S, with per-entity UniProt accessions, bound ligands, methods, resolutions and modelled residue ranges resolved against the RCSB search and data GraphQL APIs

     RCSB Protein Data Bank · RCSB PDB 2026
     used by KAT7 / HBO1 — an enzyme, a leukaemia-stem-cell dependency, and an inhibitor already in a crystal
351. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     ChEMBL database version 34, target CHEMBL3774299 (histone acetyltransferase KAT7): target_search, get_bioactivity and get_mechanism queries

     EMBL-EBI ChEMBL · ChEMBL 2026
     used by KAT7 / HBO1 — an enzyme, a leukaemia-stem-cell dependency, and an inhibitor already in a crystal
352. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42575441
     ATR-dependent phosphorylation of the histone acetyltransferase HBO1 suppresses chromatin binding and promotes replication stress responses.

     Zong C, Zhang J, Zhang Z, Cai Y, Wang Y, Fang Y, Zheng G, Li Q, Wang L, Shen J · J Biol Chem 2026
     used by KAT7 / HBO1 — an enzyme, a leukaemia-stem-cell dependency, and an inhibitor already in a crystal
353. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9H7Z6 (KAT8_HUMAN) - subcellular location with evidence codes, fetched 2026-09-20

     UniProt Consortium · UniProtKB 2026
     used by KAT8/MOF is not only a chromatin enzyme: a measured mitochondrial pool binds mtDNA, and the chromatin address depends on which complex it is in
354. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42560720
     Whack-a-menin: zifto's preclinical activity and mutant MEN1

     Bernt KM · Blood 2026
     used by Kathrin Bernt (University of Pennsylvania / Children's Hospital of Philadelphia) — DOT1L and H3K79 methylation in KMT2A-rearranged leukemia
355. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O60341 (KDM1A_HUMAN), Lysine-specific histone demethylase 1A

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by KDM1A (LSD1) — acts at the loci the fusion binds, spares normal stem cells, and still has never been shown to touch the fusion protein
356. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed E-utilities esearch record count for (MLL OR KMT2A) AND (KDM1A OR LSD1 OR AOF2 OR BHC110), run for this beat

     · NCBI PubMed, queried 2026-09-19 2026
     used by KDM1A (LSD1) — acts at the loci the fusion binds, spares normal stem cells, and still has never been shown to touch the fusion protein
357. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9Y2K7 (KDM2A_HUMAN), Lysine-specific demethylase 2A / CXXC-type zinc finger protein 8 / FBXL11

     UniProt Consortium · UniProtKB 2026
     used by KDM2A - the CXXC reader that antagonises KMT2A leukaemogenesis, and displaces wild-type MLL rather than the fusion
358. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     ChEMBL database version 34, target CHEMBL3779760 (Lysine-specific demethylase 2B): target_search, get_bioactivity and get_mechanism queries

     EMBL-EBI ChEMBL · ChEMBL 2026
     used by KDM2B — 513 potent ChEMBL rows that are mostly patent bins, and no structure of the domain they claim to inhibit
359. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
     NCBI GEO GSE260742, GSM8123392 / GSM8123393 / GSM8123394 (MLLAF9 KDM2B ChIP-seq, DMSO / SGC0946 5 uM / VTP50469 500 nM), re-binned to 2 kb from the deposited igvtools .tdf

     · NCBI Gene Expression Omnibus 2026
     used by KDM2B, the PRC1.1 CpG-island recruiter, sits at the 99.7th percentile of its own distribution on the fusion's strongest sites in DMSO and does not gain share under either a menin inhibitor or a DOT1L inhibitor - it holds position while comparable bins drift down
360. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
     NCBI GEO GSE260742 locus table over UCSC mm10 refGene windows, analyses/q117-gained-fusion-occupancy/locus-table.json

     · NCBI Gene Expression Omnibus 2026
     used by KDM2B, the PRC1.1 CpG-island recruiter, sits at the 99.7th percentile of its own distribution on the fusion's strongest sites in DMSO and does not gain share under either a menin inhibitor or a DOT1L inhibitor - it holds position while comparable bins drift down
361. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O94953 (KDM4B_HUMAN), Lysine-specific demethylase 4B

     UniProt Consortium · UniProt 2026
     used by KDM4B (JMJD2B) - the weakest of the four H3K9me3 demethylases, one of the two erasers knocked down in the only KDM4-perturbation arm in any archive that touches this mark
362. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Cellosaurus entry CVCL_0095 (SEM)

     Bairoch A; SIB Swiss Institute of Bioinformatics · Cellosaurus 2026
     used by KDM4C (JMJD2C/GASC1) — recruited by the retained KMT2A N-terminus, drugged in a KMT2A::AFF1 line, and invisible to CRISPR, One experiment that decides whether KDM4C is a target or the KDM4 family is: paralogue rescue of SD70 sensitivity in SEM, SEM (CVCL_0095) — the workhorse, from a five-year-old, and microsatellite unstable
363. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     gnomAD v4 loss-of-function constraint for KDM4C (ENSG00000107077) via the gnomAD GraphQL API

     Genome Aggregation Database, Broad Institute · gnomAD 2026
     used by KDM4C (JMJD2C/GASC1) — recruited by the retained KMT2A N-terminus, drugged in a KMT2A::AFF1 line, and invisible to CRISPR
364. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9H3R0 (KDM4C_HUMAN), lysine-specific demethylase 4C

     UniProt Consortium · UniProt 2026
     used by KDM4C (JMJD2C/GASC1) — recruited by the retained KMT2A N-terminus, drugged in a KMT2A::AFF1 line, and invisible to CRISPR
365. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     UniProtKB P29375 (KDM5A_HUMAN): sequence length, domain, zinc-finger, DNA-binding, repeat, motif and region features, and PDB cross-references

     UniProt Consortium · UniProtKB 2026
     used by KDM5A (JARID1A / RBP2 H3K4 demethylase) domain architecture
366. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P29375 (KDM5A_HUMAN) - Lysine-specific demethylase 5A, Homo sapiens

     UniProt Consortium · UniProt Knowledgebase 2026
     used by KDM5A / JARID1A / RBP2 (P29375, 1,690 aa) - already in this graph as the 3' half of NUP98::KDM5A and never written as a gene: the H3K4 demethylase CTCF recruits to a break, the only ERASER in the licensing cascade, and the one cascade member with no blood-lineage ChIP-seq anywhere
367. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     ENCODE Portal experiment search, type=Experiment, assay_title=TF ChIP-seq, status=released, target.label=KDM5A

     ENCODE Project Consortium · ENCODE Portal 2026
     used by KDM5A / JARID1A / RBP2 (P29375, 1,690 aa) - already in this graph as the 3' half of NUP98::KDM5A and never written as a gene: the H3K4 demethylase CTCF recruits to a break, the only ERASER in the licensing cascade, and the one cascade member with no blood-lineage ChIP-seq anywhere
368. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI E-utilities esearch over PubMed, db=pubmed, querytranslation read back for every query

     National Center for Biotechnology Information · NCBI Entrez Programming Utilities 2026
     used by KDM5A / JARID1A / RBP2 (P29375, 1,690 aa) - already in this graph as the 3' half of NUP98::KDM5A and never written as a gene: the H3K4 demethylase CTCF recruits to a break, the only ERASER in the licensing cascade, and the one cascade member with no blood-lineage ChIP-seq anywhere
369. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed searches for KDM6A/UTX in MLL1 and KMT2A-fusion complexes, conducted for this graph on 2026-09-18; no primary study retrieved

     Oncofusion Knowledge Graph project, using the NCBI PubMed E-utilities · Literature search 2026
     used by KDM6A / UTX — a commonly asserted KMT2A partner that belongs to a different complex and points the opposite way
370. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed human record O15054 (KDM6B) - gene_primary, protein name and length, fetched 2026-09-20

     UniProt Consortium; query run by this project · Database 2026
     used by KDM6B (JMJD3) - UTX's paralogue, which this graph has argued about for cycles without writing
371. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q07666 (KHDR1_HUMAN), human KHDRBS1, 443 aa

     · UniProt Consortium 2026
     used by KHDRBS1 (Sam68) — an RNA-binding protein that holds the MLL-AF4 message DOWN, a class no dropout screen can find
372. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q07666 (KHDR1_HUMAN), SUBCELLULAR LOCATION comment with all evidence codes, sources and note, plus TISSUE SPECIFICITY, fetched live 2026-09-21

     UniProt Consortium · Databases 2026
     used by KHDRBS1 (Sam68) — an RNA-binding protein that holds the MLL-AF4 message DOWN, a class no dropout screen can find
373. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q5VWX1 (KHDR2_HUMAN), human KHDRBS2, 349 aa

     · UniProt Consortium 2026
     used by KHDRBS2 (SLM1) — a counted absence: zero leukaemia records over five aliases, in a family that regulates the MLL-AF4 message
374. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O75525 (KHDR3_HUMAN), human KHDRBS3, 346 aa

     · UniProt Consortium 2026
     used by KHDRBS3 (SLM2/T-STAR) — the third STAR paralogue, also zero leukaemia records, also flat in DepMap
375. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.reviewPMID 42349662
     Mixed phenotype acute leukemia: Lineage assignment, immunophenotypic classification and genetic insights.

     Leventaki V, Wang SA · Hum Pathol 2026
     used by KIT / CD117 - the most myeloid-specific antigen in the lineage-assignment panel, and the mutation that is mutually exclusive with KMT2A rearrangement
376. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P10721 (KIT_HUMAN), Mast/stem cell growth factor receptor Kit, SCFR, EC 2.7.10.1, CD antigen CD117, 976 aa, single reviewed human record, primary gene name KIT

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by KIT / CD117 - the most myeloid-specific antigen in the lineage-assignment panel, and the mutation that is mutually exclusive with KMT2A rearrangement
377. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P21583 (SCF_HUMAN) - Kit ligand

     · UniProtKB 2026
     used by KITLG (stem cell factor) - the niche ligand of KIT, zero mentions anywhere in this graph, and its own symbol collides with the SCF ubiquitin ligase this corpus talks about constantly, Niche proteins enumerated and NOT written in this tranche, and four symbol traps measured while doing it - three of them new to the registry
378. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     DepMap CRISPR (Chronos) gene effect and gnomAD constraint, retrieved via the Open Targets Platform GraphQL API and the gnomAD GraphQL API

     Broad Institute DepMap; gnomAD; Open Targets · Databases 2026
     used by KMT2A / MLL1 — the gene that breaks, Phase-2 dossier: the CXXC-DNA interface - two structures, a genetically validated requirement, and a selectivity problem that decides everything
379. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     PDBe SIFTS best_structures mapping for UniProt Q03164

     · EMBL-EBI PDBe API 2026
     used by KMT2A / MLL1 — the gene that breaks
380. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     Human Protein Atlas - KMT2A (ENSG00000118058), machine-readable gene record

     Human Protein Atlas consortium · proteinatlas.org 2026
     used by KMT2A / MLL1 — the gene that breaks, The cell types that need MLL1 are the uncommitted ones - dependence ends exactly where lineage commitment begins
381. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset
     PRIDE Archive PXD006201 - Characterisation of protein ubiquitination using UbiSite technology

     · PRIDE Archive, EMBL-EBI 2026
     used by KMT2A K1130 ubiquitination - the same retained lysine as the clock acetylation site, carrying a chemically exclusive second mark that no KMT2A paper has ever mentioned
382. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted-absence searches for FA genes against KMT2A/MLL, run 2026-09-20 with aliases and title-checked

     · PubMed (NCBI) 2026
     used by KMT2A rearrangement creates a requirement for the FA ubiquitin-transfer module — the claim, its prior, and the four results that would kill it
383. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     IntAct molecular interaction database, REST findInteractions on Q03164 (KMT2A), 376 records retrieved 2026-09-23 by Q129

     · IntAct (EMBL-EBI) 2026
     used by KMT2A-ABT1 is one spoke-expanded BioPlex 3.0 AP-MS row in HEK293T in which ABT1 is the bait and KMT2A the prey, and ABT1's nucleolus is ECO:0000250 only - declined, KMT2A-ANOS1 is one spoke-expanded BioPlex 3.0 AP-MS row with ANOS1 - a secreted, cell-membrane axon-guidance protein - as the bait and KMT2A as the prey in HEK293T - declined, KMT2A-FGFBP1 is spoke-expanded BioPlex 3.0 AP-MS recovered in BOTH HEK293T and HCT116 - it passes BioPlex's own replication criterion and the partner is a secreted extracellular protein - declined, KMT2A-KRR1 is one spoke-expanded BioPlex 3.0 AP-MS row in HEK293T with KRR1 as bait and KMT2A as prey, sitting in a seven-member ribosomal block at the floor score - declined, KMT2A-OASL is one spoke-expanded BioPlex 3.0 AP-MS row with OASL as bait and KMT2A as prey; OASL is the only partner in the beat natively expressed in blood leukocytes, and its nucleolar annotation is uncoded - declined, with the compartment argument unavailable, KMT2A-PRKRA is one spoke-expanded BioPlex 3.0 AP-MS row with PRKRA (PACT) as bait and KMT2A as prey; PRKRA's only UniProt compartments are cytoplasm and perinuclear region, both uncoded - declined, KMT2A-TMCO1 is a single DSSO crosslink in one detergent fraction of isolated U2OS nuclei with no bait on either side; TMCO1 is an ER-membrane calcium channel and the source paper attributes 4% of its links to nucleus-ER contamination - declined, The ABT1/KRR1/UTP3 nucleolar triple: pre-registered, then adjudicated - it is not three proteins on two baits but a seven-member ribosomal block in one screen plus one hit in a neighbourhood that shows no nucleolar enrichment, and two of the four pre-registered discriminators were void exactly as the pre-registration predicted, The missing reagent: a KMT2A-fusion or wild-type-KMT2A proximity bait in a KMT2A-rearranged leukaemia line - IntAct has curated no KMT2A-bait interaction experiment since April 2015 and no PSIP1-bait since October 2012, The REST-wide direction audit Q104 asked for: scaffold-as-bait rows DO exist in the 36% of the record PSICQUIC hides - KMT2A is a bait in 96 of 376 rows across 18 publications and PSIP1 in 11 of 114 across 4, but the most recent is 2015 and 2012, and none of the thirteen never-discussed partners comes from one
384. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q9ULW3 (ABT1): primary gene name, sequence length, subcellular location and function, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by KMT2A-ABT1 is one spoke-expanded BioPlex 3.0 AP-MS row in HEK293T in which ABT1 is the bait and KMT2A the prey, and ABT1's nucleolus is ECO:0000250 only - declined, The ABT1/KRR1/UTP3 nucleolar triple: pre-registered, then adjudicated - it is not three proteins on two baits but a seven-member ribosomal block in one screen plus one hit in a neighbourhood that shows no nucleolar enrichment, and two of the four pre-registered discriminators were void exactly as the pre-registration predicted
385. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     IntAct molecular interaction database, REST findInteractions totalElements for Q9ULW3, Q13601, Q9NQZ2, P61964 and O00255, retrieved 2026-09-23 by Q129

     · IntAct (EMBL-EBI) 2026
     used by KMT2A-ABT1 is one spoke-expanded BioPlex 3.0 AP-MS row in HEK293T in which ABT1 is the bait and KMT2A the prey, and ABT1's nucleolus is ECO:0000250 only - declined
386. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset
     analyses/q160-the-prey-only-interactome/rest-roles.json, experimentalRole tallies over the 212 human prey-only partners, generated 2026-09-24

     · this project 2026
     used by KMT2A-AKAP8 (AKAP95): graded 'prey-only' by this project, and it is a direct positive modulator of MLL H3K4 methyltransferase activity from a dedicated MLL paper - ADMITTED
387. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P23352 (ANOS1): primary gene name, sequence length, subcellular location and function, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by KMT2A-ANOS1 is one spoke-expanded BioPlex 3.0 AP-MS row with ANOS1 - a secreted, cell-membrane axon-guidance protein - as the bait and KMT2A as the prey in HEK293T - declined, KMT2A-KRR1 is one spoke-expanded BioPlex 3.0 AP-MS row in HEK293T with KRR1 as bait and KMT2A as prey, sitting in a seven-member ribosomal block at the floor score - declined
388. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry O15516 (CLOCK_HUMAN), subcellular location and tissue specificity, retrieved 2026-09-24

     · UniProt Consortium 2026
     used by KMT2A-CLOCK: one paper, six IntAct records, and the bait/prey grade splits it down the middle - CLOCK falls in the discard bin and SIRT1 does not, from the same experiments
389. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset
     analyses/q160-the-prey-only-interactome/census.json, corpus_mentions field, generated 2026-09-24

     · this project 2026
     used by KMT2A-DRC5 - DECLINED. A ciliary dynein-regulatory-complex protein, recovered by BioID in a centrosome-cilium map, and the only one of 135 uncovered partners never mentioned anywhere in this corpus
390. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     UniProtKB Q05925 (HME1_HUMAN / EN1) and Human Protein Atlas v25.1 record for EN1 (ENSG00000163064), both retrieved 2026-09-23

     2026
     used by KMT2A-EN1 declined: one spoke-expanded BioID row from an ectopic neural homeobox construct in a kidney cell, and the only screen that ever looked found EN1 unexpressed in AML lines
391. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     NCBI PubMed esearch via scripts/pubmed_safe.py, run 2026-09-23; querytranslations recorded: "EN1"[Title/Abstract] AND "KMT2A"[Title/Abstract] and "EN1"[Title/Abstract] AND "MLL"[Title/Abstract]

     2026
     used by KMT2A-EN1 declined: one spoke-expanded BioID row from an ectopic neural homeobox construct in a kidney cell, and the only screen that ever looked found EN1 unexpressed in AML lines
392. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q14512 (FGFBP1): primary gene name, sequence length, subcellular location, function and tissue specificity, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by KMT2A-FGFBP1 is spoke-expanded BioPlex 3.0 AP-MS recovered in BOTH HEK293T and HCT116 - it passes BioPlex's own replication criterion and the partner is a secreted extracellular protein - declined
393. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P82970, subcellular location, length and tissue specificity, retrieved 2026-09-24

     · UniProt Consortium 2026
     used by KMT2A-HMGN5: recovered by endogenous CRISPR tagging in OpenCell, not by over-expression - a chromatin-decompacting nucleosome binder with a real reason to be near KMT2A
394. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q53GT1, subcellular location, length and tissue specificity, retrieved 2026-09-24

     · UniProt Consortium 2026
     used by KMT2A-KLHL22 - DECLINED. The single source is a cryo-EM structure of KLHL22-CUL3 bound to glutamate dehydrogenase, and KMT2A is a HEK293F pull-down passenger with no nuclear rationale
395. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q13601 (KRR1): primary gene name, sequence length, subcellular location and function, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by KMT2A-KRR1 is one spoke-expanded BioPlex 3.0 AP-MS row in HEK293T with KRR1 as bait and KMT2A as prey, sitting in a seven-member ribosomal block at the floor score - declined
396. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     NCBI GEO DataSets search, 2026-09-24

     NCBI Gene Expression Omnibus · NCBI GEO 2026
     used by KMT2A-N/C CUT&RUN on one untreated KMT2A::AFF1 blast from outside Texas Children's, scored at the six AFF1-exclusive gene bodies with a pre-declared margin column
397. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q15646 (OASL): primary gene name, sequence length, subcellular location with evidence codes, function and tissue specificity, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by KMT2A-OASL is one spoke-expanded BioPlex 3.0 AP-MS row with OASL as bait and KMT2A as prey; OASL is the only partner in the beat natively expressed in blood leukocytes, and its nucleolar annotation is uncoded - declined, with the compartment argument unavailable
398. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry O75569 (PRKRA): primary gene name, sequence length, subcellular location with evidence codes, and function, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by KMT2A-PRKRA is one spoke-expanded BioPlex 3.0 AP-MS row with PRKRA (PACT) as bait and KMT2A as prey; PRKRA's only UniProt compartments are cytoplasm and perinuclear region, both uncoded - declined
399. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Cancer Stat Facts: Leukemia - Acute Myeloid Leukemia (AML)

     National Cancer Institute Surveillance, Epidemiology, and End Results Program · SEER 2026
     used by KMT2A-rearranged acute leukemia across all ages: infants are 4% of it
400. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Cancer Stat Facts: Leukemia - Acute Lymphocytic Leukemia (ALL)

     National Cancer Institute Surveillance, Epidemiology, and End Results Program · SEER 2026
     used by KMT2A-rearranged acute leukemia across all ages: infants are 4% of it
401. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 41126738
     Age-specific mutation profiles and their prognostic implications in pediatric KMT2A-rearranged acute myeloid leukemia

     Shoji K, et al. · Haematologica 2026
     used by KMT2A-rearranged acute myeloid leukaemia in children and infants
402. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed E-utilities esearch record counts for DSIF and NELF subunits and aliases against KMT2A and MLL, run for this beat

     · NCBI PubMed, queried 2026-09-19 2026
     used by KMT2A-rearranged cells need the factors retained through elongation MORE and the factors ejected at pause release LESS — a six-gene asymmetry nobody has reported, NELF — the brake that has to come off for elongation, absent from the KMT2A literature, and less required in KMT2A-rearranged lines than in any other leukaemia
403. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entries Q9UM00 (TMCO1) and Q03164 (KMT2A): primary gene name, sequence length, subcellular location with evidence codes, function and tissue specificity, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by KMT2A-TMCO1 is a single DSSO crosslink in one detergent fraction of isolated U2OS nuclei with no bait on either side; TMCO1 is an ER-membrane calcium channel and the source paper attributes 4% of its links to nucleus-ER contamination - declined
404. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     IntAct molecular interaction database, REST findInteractions free-text query on 30021884, all 4,856 rows paginated and role-counted 2026-09-23 by Q129

     · IntAct (EMBL-EBI) 2026
     used by KMT2A-TMCO1 is a single DSSO crosslink in one detergent fraction of isolated U2OS nuclei with no bait on either side; TMCO1 is an ER-membrane calcium channel and the source paper attributes 4% of its links to nucleus-ER contamination - declined, PSIP1-GDF5 is a single DSSO crosslink in isolated U2OS nuclei with no bait on either side; GDF5 is a secreted cartilage growth factor, and the source paper itself attributes 30% of its cross-compartment links to contamination during nuclei isolation - declined
405. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     IntAct PSICQUIC endpoint, queried 2026-09-21: pubid:29777171 = 0 rows; positive control pubid:33961781 = 1,000 rows; 26 distinct PMIDs enumerated from the 161 rows of id:Q03164, with 29777171 not among them.

     · IntAct (EMBL-EBI), PSICQUIC MITAB 2.7 2026
     used by KMT2A::AFF1 has had a published affinity-purification interactome since 2018 — in a paper titled for SETD2, uncurated by IntAct, and cited zero times here
406. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 41681872
     Impact of Fusion Partners and Transplantation Benefit in Intensively Treated KMT2A-Rearranged Acute Myeloid Leukemia.

     Shen H, Chen J, et al. · Cancers (Basel) 2026
     used by KMT2A::ELL in adult AML: the one partner that separates, in two independent adult cohorts, One karyotype band, two partner genes: why t(11;19) and t(10;11) can cancel a real partner effect, Which partner, in which patient: KMT2A partner frequencies across six age-lineage strata
407. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P42566 (EPS15_HUMAN) Epidermal growth factor receptor substrate 15, Homo sapiens, 896 aa

     UniProt Consortium · UniProtKB 2026
     used by KMT2A::EPS15 (MLL-AF1p), t(1;11)(p32;q23) — the infant-ALL cytoplasmic partner
408. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI E-utilities esearch over PubMed, query (MLL[Title/Abstract] OR KMT2A[Title/Abstract]) AND (gephyrin[Title/Abstract] OR GPHN[Title/Abstract]), run 2026-09-19, 3 records, all three titles read

     US National Library of Medicine, PubMed · PubMed (E-utilities) 2026
     used by KMT2A::GPHN (MLL-gephyrin), t(11;14)(q23;q24) — the 15-residue counterexample
409. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q8IZL2 (MAML2_HUMAN) and InterPro Pfam domain boundaries for MAML2

     UniProt Consortium; InterPro (EMBL-EBI) · UniProtKB / InterPro 2026
     used by KMT2A::MAML2 keeps MAML2's activation domain and loses its Notch-binding domain, and suppresses Notch output, MAML2 exon 2: the strongly preferred 3' acceptor, the same in leukaemia, thymoma and salivary-gland tumours
410. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.paperPMID 41834483
     Secondary T-Lymphoblastic Lymphoma With KMT2A::MAML2 Rearrangement Following Myeloid Sarcoma and RUNX1::RUNX1T1-Positive Acute Myeloid Leukemia.

     Li T, Wang A, Wu P, Sun H, Zhang L, Chen M, Zhao X, Wang H · Pediatric Blood & Cancer 2026
     used by KMT2A::MAML2, inv(11)(q21q23) - a therapy-related fusion that also causes a solid tumour
411. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI E-utilities esearch over PubMed, query (MLL[Title/Abstract] OR KMT2A[Title/Abstract]) AND MYO1F[Title/Abstract], run 2026-09-19, 2 records, both titles read

     US National Library of Medicine, PubMed · PubMed (E-utilities) 2026
     used by KMT2A::MYO1F, t(11;19)(q23;p13.2) — recurrent in infant AML, and never functionally tested, MYO1F — unconventional myosin IF, a KMT2A partner with neither a transactivation domain nor a dimerisation domain
412. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9NVA2 (SEP11_HUMAN) Septin-11, Homo sapiens, 429 aa

     UniProt Consortium · UniProtKB 2026
     used by KMT2A::SEPTIN11 (MLL-SEPT11) — the fusion that cytogenetically impersonates t(4;11), SEPTIN11 (septin-11) — KMT2A fusion partner at 4q21, adjacent to AFF1
413. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q15019 (SEPT2_HUMAN) Septin-2 / NEDD5, Homo sapiens, 361 aa

     UniProt Consortium · UniProtKB 2026
     used by KMT2A::SEPTIN2 (MLL-SEPT2), t(2;11)(q37;q23) — the therapy-related septin, SEPTIN2 (septin-2 / NEDD5) — KMT2A fusion partner in t(2;11)(q37;q23)
414. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q99719 (SEPT5_HUMAN) Septin-5 / CDCrel-1, Homo sapiens, 369 aa

     UniProt Consortium · UniProtKB 2026
     used by KMT2A::SEPTIN5 (MLL-SEPT5 / MLL-hCDCrel-1), t(11;22)(q23;q11.2), SEPTIN5 (septin-5 / CDCrel-1) — KMT2A fusion partner in t(11;22)(q23;q11.2)
415. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q14141 (SEPT6_HUMAN) Septin-6, Homo sapiens, 434 aa

     UniProt Consortium · UniProtKB 2026
     used by KMT2A::SEPTIN6 (MLL-SEPT6), t(X;11)(q24;q23) and its cryptic insertion variants, SEPTIN6 (septin-6) — cytoskeletal GTPase, KMT2A fusion partner in t(X;11)(q24;q23)
416. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9UHD8 (SEPT9_HUMAN) Septin-9 / MLL septin-like fusion protein MSF-A, Homo sapiens, 586 aa

     UniProt Consortium · UniProtKB 2026
     used by KMT2A::SEPTIN9 (MLL-SEPT9 / MLL-MSF), t(11;17)(q23;q25), SEPTIN9 (septin-9 / MSF) — cytoskeletal GTPase, KMT2A fusion partner in t(11;17)(q23;q25)
417. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch counts for KMT2A/USP2/menin intersection queries, run 2026-09-19

     National Center for Biotechnology Information (NCBI), PubMed · PubMed (NCBI E-utilities) 2026
     used by KMT2A::USP2, inv(11)(q23.3q23.3) - the minor-BCR fusion that keeps the PHD fingers, Menin inhibitors are prescribed on 'KMT2A-rearranged', a category that contains proteins as different as KMT2A::AFF1 and KMT2A::USP2
418. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P40818 (UBP8_HUMAN), Ubiquitin carboxyl-terminal hydrolase 8, with domain boundaries

     UniProt Consortium · UniProtKB 2026
     used by KMT2A::USP8, t(11;15)(q23;q21) - three patients, and the second instance of a deubiquitinase partner, USP8 (UBPY) - the second deubiquitinase KMT2A partner, three patients, same UCH logic
419. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     analyses/is-kmt2a-proximity-promiscuity-just-size/results.json and analyses/interactome-tail-size-and-abundance-adjudication/overdispersion.json (this repository)

     2026
     used by KMT2A's proximity promiscuity is BAIT-CLASS-SPECIFIC: it is recovered at twice its size-and-abundance prediction by RNA-binding-protein baits in a leukaemia cell and at exactly its prediction by transcription-factor baits in a kidney cell, Prey recovery in the two BioID depositions tracks SIZE and not abundance - and the interactome tail was being scored on the wrong side of the pair, because every one of the 22 partners is the BAIT and every core protein is the PREY
420. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed human records Q9UMN6 (KMT2B), O14686 (KMT2D), Q8NEZ4 (KMT2C), Q8IZD2 (KMT2E), Q03164 (KMT2A), O15047 (SETD1A), Q9UPS6 (SETD1B) - gene_primary, length and canonical sequence, fetched 2026-09-20

     UniProt Consortium; queries and alignment by this project · Database 2026
     used by KMT2B (MLL2/MLL4) - the other protein menin binds, and the one this graph never wrote, MLL2 and MLL4 each name two different genes, and the ambiguity is in the papers, not in the databases
421. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 41032751
     Fetal context conveys heritable protection against MLL-rearranged AML that depends on MLL3.

     Mendoza-Castrejon J, Yang W, Denby E, et al. · Blood 2026
     used by KMT2C (MLL3) - the fetal brake on MLL-rearranged leukaemia, and a 7q tumour suppressor chemotherapy selects against
422. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed human record Q8NEZ4 (KMT2C) - gene_primary, length and canonical sequence, fetched 2026-09-20

     UniProt Consortium; query run by this project · Database 2026
     used by KMT2C (MLL3) - the fetal brake on MLL-rearranged leukaemia, and a 7q tumour suppressor chemotherapy selects against
423. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     UniProtKB Q8NEZ4 (KMT2C_HUMAN) SUBCELLULAR LOCATION comment, fetched 2026-09-21

     · UniProt Consortium 2026
     used by KMT2C (MLL3) - the fetal brake on MLL-rearranged leukaemia, and a 7q tumour suppressor chemotherapy selects against
424. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     Human Protein Atlas v25.1, subcellular (immunofluorescence) and Blood Atlas records for KMT2C, fetched 2026-09-21

     · Human Protein Atlas 2026
     used by KMT2C (MLL3) - the fetal brake on MLL-rearranged leukaemia, and a 7q tumour suppressor chemotherapy selects against
425. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed human records O14686 (KMT2D) and Q9UMN6 (KMT2B) - gene_primary, gene synonyms, protein names and length, fetched 2026-09-20

     UniProt Consortium; queries run by this project · Database 2026
     used by KMT2D (MLL2/MLL4) - the gene named in this graph's menin-resistance entry, written here for the first time
426. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     UniProtKB O14686 (KMT2D_HUMAN) SUBCELLULAR LOCATION comment, fetched 2026-09-21

     · UniProt Consortium 2026
     used by KMT2D (MLL2/MLL4) - the gene named in this graph's menin-resistance entry, written here for the first time
427. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 42409830
     The H3K4 methyltransferase KMT2D is an essential cofactor for GATA1 at erythroid gene enhancers.

     · Nat Commun 2026
     used by KMT2D (MLL2/MLL4) - the gene named in this graph's menin-resistance entry, written here for the first time
428. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
     Human Protein Atlas v25.1, subcellular (immunofluorescence) and Blood Atlas records for KMT2D, fetched 2026-09-21

     · Human Protein Atlas 2026
     used by KMT2D (MLL2/MLL4) - the gene named in this graph's menin-resistance entry, written here for the first time
429. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed human record Q8IZD2 (KMT2E) - gene_primary, protein name and length, fetched 2026-09-20

     UniProt Consortium; query run by this project · Database 2026
     used by KMT2E (MLL5) - the family member with a dead SET domain, and the exclusion from COMPASS is justified
430. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Cellosaurus record CVCL_7972 (KOPB-26)

     · Cellosaurus (SIB) 2026
     used by KOPB-26 (CVCL_7972): a t(9;11) B-ALL line from a 13-month-old, and the model for 42% of this partner's patients that nobody uses
431. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Cellosaurus cell line KOPN-8 (CVCL_1866)

     Bairoch A, et al.; Cellosaurus · Cellosaurus (SIB) 2026
     used by KOPN-8 (CVCL_1866): the field's default KMT2A::MLLT1 line, and its fusion protein has no YEATS domain
432. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 41849234
     Discovery and preclinical activity of the menin-KMT2A inhibitor ziftomenib in acute leukemia models.

     Miao H, Wu T, Purohit T, Chen D, et al. · Blood 2026
     used by KOPN-8 (CVCL_1866): the field's default KMT2A::MLLT1 line, and its fusion protein has no YEATS domain, Menin dependence of KMT2A::MLLT1: real, repeatedly demonstrated, and always as one lane of a partner panel, Revumenib (SNDX-5613, Revuforj) — first approved menin–KMT2A interface inhibitor, Ziftomenib (KO-539, Komzifti) — once-daily menin inhibitor approved in NPM1-mutant AML
433. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 41711432
     Menin inhibitors display differential in vitro sensitivity in KMT2A-rearranged infant acute lymphoblastic leukemia.

     Dymock SCC, Oommen J, Malinge S, Cheung LC, Kotecha RS · Leuk Lymphoma 2026
     used by Kotecha group, Perth: the infant KMT2A-rearranged laboratory this graph had cited once, Papers we know exist, know matter, and cannot read, The state under menin inhibition — differentiation in AML, rapid death in ALL, and a GMP-like exit in the cells that switch lineage instead, Treating the five menin inhibitors as one drug, when a 2026 title says they are not
434. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42085603
     Combining menin and MEK inhibition to target poor prognosis KMT2A-rearranged RAS pathway-mutant acute myeloid leukemia.

     Scheidegger N, Schneider C, Alexe G, et al. · Blood Advances 2026
     used by KRAS - the commonest co-mutation in a disease that has almost none, and it is usually in a minority of the cells, No second driver means no second target - the quiet genome forecloses the combination logic that works in every other leukaemia, Track the sub-1% cooperating-lesion clones through menin inhibition, because nobody has measured what the drug selects for, Treating a subclonal lesion is selection pressure applied to the clone you did not aim at
435. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P01116 (RASK_HUMAN) - SUBCELLULAR LOCATION comment block with evidence codes, including the isoform 2B comment

     · UniProt Consortium 2026
     used by KRAS - the commonest co-mutation in a disease that has almost none, and it is usually in a minority of the cells
436. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.news
     Kura Oncology pipeline page (ziftomenib programme and Kyowa Kirin collaboration)

     Kura Oncology, Inc. · kuraoncology.com 2026
     used by Kura Oncology — ziftomenib (KO-539): an adults-only sponsor that quietly supplies infant trials
437. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     GTEx v8 median gene expression, LAMP5 (ENSG00000125869.9) across 54 tissues: Brain_Nucleus_accumbens_basal_ganglia 323.89 TPM, Brain_Caudate_basal_ganglia 134.31, Brain_Putamen_basal_ganglia 85.09, Brain_Frontal_Cortex_BA9 48.51, whole-body median 1.21 TPM. Fetched 2026-09-23 via gtexportal.org API v2

     · GTEx Portal 2026
     used by LAMP5 (BAD-LAMP) - a direct MLL-fusion target gene, a proposed immunotherapy antigen, and a brain protein, LAMP5 was proposed as an immunotherapy target for MLL-rearranged leukaemia without a normal-tissue filter; two atlases independently put it above 290 in the basal ganglia, and it is not partner-specific either, LAMP5-directed therapy for KMT2A-rearranged leukaemia would meet the basal ganglia, in a disease treated in infants and routinely treated into the CNS
438. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9UJQ1 (LAMP5_HUMAN), lysosome-associated membrane glycoprotein 5 / BAD-LAMP, 280 aa, Cell membrane with TOPO_DOM 30-235 Extracellular; release 2026_03, fetched 2026-09-23

     · UniProt 2026
     used by LAMP5 (BAD-LAMP) - a direct MLL-fusion target gene, a proposed immunotherapy antigen, and a brain protein, LAMP5 was proposed as an immunotherapy target for MLL-rearranged leukaemia without a normal-tissue filter; two atlases independently put it above 290 in the basal ganglia, and it is not partner-specific either
439. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q86U70 (LDB1_HUMAN), LIM domain-binding protein 1, feature table and sequence

     UniProt Consortium · UniProtKB 2026
     used by LDB1 (Q86U70) - and the sarcoma fusion keeps the part that self-associates while losing the LIM interaction domain entirely
440. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Ensembl REST API lookup, LDB1 (ENSG00000198728), canonical transcript ENST00000673968 with exon and translation coordinates

     Ensembl (EMBL-EBI) · Ensembl REST 2026
     used by LDB1 (Q86U70) - and the sarcoma fusion keeps the part that self-associates while losing the LIM interaction domain entirely
441. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9UJU2 (LEF1_HUMAN), Lymphoid enhancer-binding factor 1 — accession, primary gene name, length and subcellular-location comment retrieved 2026-09-24

     · UniProt Consortium, EMBL-EBI/SIB/PIR 2026
     used by LEF1 — the Wnt/β-catenin DNA-binding factor of the T-lineage, named as an MLL-AF4-specific interactor in a T-ALL cell line and with essentially no B-lineage or KMT2A literature
442. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed search for LEO1 in the context of KMT2A/MLL-fusion leukemia, conducted for this graph on 2026-09-18; no primary subunit-level study retrieved

     Oncofusion Knowledge Graph project, using the NCBI PubMed E-utilities · Literature search 2026
     used by LEO1 — the weakest-evidenced entry in the PAF1 complex, and the gene whose Ensembl id this project already got wrong once
443. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     UniProtKB Q8WVC0 (LEO1_HUMAN) feature table and PDB cross-references; RCSB entries 6TED, 7OPC and 8A3Y verified via the RCSB data API

     UniProt Consortium; RCSB Protein Data Bank · Databases 2026
     used by LEO1 — the weakest-evidenced entry in the PAF1 complex, and the gene whose Ensembl id this project already got wrong once
444. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P48357 (LEPR_HUMAN) - Leptin receptor; and O15243 (OBRG_HUMAN) - LEPROT

     · UniProtKB 2026
     used by LEPR - the marker that defines the SCF-supplying perivascular niche cell, the receptor for an adipocyte signal that blunts cytarabine, and a gene_exact query that returns the wrong protein first
445. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     HGNC REST API, gene group 1697 (MicroRNA MIRLET7 family) and fetch/symbol/MIRLET7A1

     2026
     used by let-7 microRNA family (12 HGNC loci) - the effector LIN28B blocks. CORRECTED IN-SESSION: the headline 'zero papers in KMT2A leukaemia' was a NAME-LIST ARTEFACT; searching MLL instead of KMT2A returns three, one of them directly on point
446. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI E-utilities esearch against PubMed, run through scripts/pubmed_safe.py

     2026
     used by let-7 microRNA family (12 HGNC loci) - the effector LIN28B blocks. CORRECTED IN-SESSION: the headline 'zero papers in KMT2A leukaemia' was a NAME-LIST ARTEFACT; searching MLL instead of KMT2A returns three, one of them directly on point, PROPOSED: measure let-7 and restore it in the human fetal-liver KMT2A::AFF1 model - an axis measured in mouse MLL-fusion AML but never in the index fusion
447. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     IntAct molecular interaction database (EMBL-EBI), PSICQUIC tab27 record for id:Q6ZN17 AND id:Q03164

     2026
     used by LIN28B - a one-row BioID prey of KMT2A that a 2026 Blood paper shows is REQUIRED for KMT2A::AFF1 to transform human fetal cells
448. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q6ZN17 (LN28B_HUMAN)

     2026
     used by LIN28B - a one-row BioID prey of KMT2A that a 2026 Blood paper shows is REQUIRED for KMT2A::AFF1 to transform human fetal cells, LIN28B localization - a nucleolar pool that sequesters pri-let-7, a predominantly cytoplasmic steady state with cell-cycle-dependent nuclear entry, and NO measurement in any haematopoietic cell
449. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.reviewPMID 42362807
     Plasticity under pressure: biology and detection of lineage switch in acute leukemia.

     Kovach AE, ..., Davis KL · Leukemia 2026
     used by Lineage drift - the partial state between B-ALL and AML, and the fact that nobody has published the ORDER in which markers change, Lineage switch as antigen escape from CD19-directed therapy in KMT2A-rearranged leukemia, Which marker moves first? A re-analysis of flow files that already exist, to put an order on lineage switch
450. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     IntAct molecular interaction database (EMBL-EBI), PSICQUIC tab27 record for id:O75475 AND id:P02545

     2026
     used by LMNA - LEDGF is a prey of the nuclear-envelope MARKER bait, so this row is a statement about address, not about complex membership
451. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P02545 (LMNA_HUMAN)

     2026
     used by LMNA - LEDGF is a prey of the nuclear-envelope MARKER bait, so this row is a statement about address, not about complex membership
452. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
     UniProtKB P29375 (KDM5A_HUMAN): FT REGION 1623..1690 /note='Interaction with LMO2' /evidence='ECO:0000269|PubMed:9129143'; SQ 1690 AA

     UniProt Consortium; flat file fetched by this project 2026-09-20 · Database record 2026
     used by LMO2 (rhombotin-2) - a bridging LIM-only protein, higher in pro-B and MLL-rearranged B-ALL, anti-selective in KMT2A-rearranged lines, and a physical partner of the KDM5A module that NUP98::KDM5A retains
453. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.analysis
     KMT2A 14-3-3 motif scan: does the retained fragment carry a phosphorylation-gated handle?

     · Oncofusion knowledge graph (internal analysis) 2026
     used by Looking for a second handle on the retained fragment, and not finding one
454. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI E-utilities esearch db=pubmed via scripts/pubmed_safe.py, 2026-09-23. querytranslations read back from each response: "MBTD1"[Title/Abstract] AND "KMT2A"[Title/Abstract]; "MBTD1"[Title/Abstract] AND "EZHIP"[Title/Abstract]; "MBTD1"[Title/Abstract] AND "CXorf67"[Title/Abstract]; "MBTD1"[Title/Abstract] AND "sarcoma"[Title/Abstract]. Counts and id lists persisted to analyses/q123-the-architecture-from-other-parts-analogy/bounded-searches.json

     · NCBI PubMed 2026
     used by Low-grade endometrial stromal sarcoma is a family of NuA4-acetyltransferase-to-Polycomb fusions, and that is why one of MBTD1's two fusions looks nothing like the other, ZMYND11::MBTD1 AML is menin-inhibitor sensitive despite having no KMT2A rearrangement, because the translocation deletes ZMYND11's MYND domain and with it a physical brake on wild-type KMT2A, ZMYND11::MBTD1 is the KMT2A-fusion architecture assembled from different parts - and the part it throws away is a direct physical brake on KMT2A itself
455. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
     IntAct molecular interaction database, PSICQUIC MITAB 2.7, query id:Q5S007 AND id:Q9UHB7, 1 row retrieved 2026-09-21

     · IntAct (EMBL-EBI) 2026
     used by LRRK2 - the AFF4 row is one of 78 hits on an in-vitro protein array, but the protein has a real AML literature that arrived through USP7 and interferon, not through the interactome
456. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q5S007 (LRRK2_HUMAN, Leucine-rich repeat serine/threonine-protein kinase 2), subcellular location and function comments with evidence codes

     · UniProtKB/Swiss-Prot 2026
     used by LRRK2 - the AFF4 row is one of 78 hits on an in-vitro protein array, but the protein has a real AML literature that arrived through USP7 and interferon, not through the interactome
457. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted-absence search for LRRK2 against MLL, KMT2A and leukaemia, run 2026-09-21, all ten leukaemia hits title-checked

     · PubMed (NCBI) 2026
     used by LRRK2 - the AFF4 row is one of 78 hits on an in-vitro protein array, but the protein has a real AML literature that arrived through USP7 and interferon, not through the interactome
458. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     UniProtKB - Q9NX58 (LYAR_HUMAN), Cell growth-regulating nucleolar protein

     · UniProt Knowledgebase 2026
     used by LYAR (Q9NX58) - a zinc-finger nucleolar growth regulator cloned from a T-cell leukaemia line, in six of seven MLL-fusion interactomes, and the one member of this block whose discovery system is the same lineage as the AP-MS host
459. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     NCBI PubMed esearch, bounded-absence query (counted negative)

     · NCBI E-utilities 2026
     used by LYAR (Q9NX58) - a zinc-finger nucleolar growth regulator cloned from a T-cell leukaemia line, in six of seven MLL-fusion interactomes, and the one member of this block whose discovery system is the same lineage as the AP-MS host
460. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Cell Ontology term CL:0000936 early lymphoid progenitor, retrieved via the EMBL-EBI Ontology Lookup Service OLS4 API

     EMBL-EBI Ontology Lookup Service; Cell Ontology consortium · Database 2026
     used by Lymphoid-primed multipotent progenitor (LMPP) — the bi-potent cell that explains how one fusion makes two lineages
461. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q8IZL2 (MAML2_HUMAN), Mastermind-like protein 2, with InterPro/Pfam domain boundaries

     UniProt Consortium; InterPro (EMBL-EBI) · UniProtKB / InterPro 2026
     used by MAML2 (mastermind-like 2) - the Notch co-activator that is a KMT2A partner in leukaemia and in thymoma
462. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch counts for MAML2 symbol, alias and partner queries, run 2026-09-19

     National Center for Biotechnology Information (NCBI), PubMed · PubMed (NCBI E-utilities) 2026
     used by MAML2 (mastermind-like 2) - the Notch co-activator that is a KMT2A partner in leukaemia and in thymoma
463. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed E-utilities esearch, db=pubmed, run 2026-09-20

     NCBI · PubMed 2026
     used by MAP3K14 (NIK) — the one node in this pathway where ACTIVATION, not inhibition, is the proposed therapy, and the one that also damages normal stem cells
464. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q99558 (M3K14_HUMAN), Mitogen-activated protein kinase kinase kinase 14

     UniProt Consortium · UniProt 2026
     used by MAP3K14 (NIK) — the one node in this pathway where ACTIVATION, not inhibition, is the proposed therapy, and the one that also damages normal stem cells
465. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q99558 (M3K14_HUMAN) SUBCELLULAR LOCATION and TISSUE SPECIFICITY comments, fetched 2026-09-21

     UniProt Consortium · UniProtKB 2026
     used by MAP3K14 (NIK) — the one node in this pathway where ACTIVATION, not inhibition, is the proposed therapy, and the one that also damages normal stem cells
466. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O95819 (M4K4_HUMAN) gene synonyms, SUBCELLULAR LOCATION and length, fetched 2026-09-21

     UniProt Consortium · UniProtKB 2026
     used by MAP3K14 (NIK) — the one node in this pathway where ACTIVATION, not inhibition, is the proposed therapy, and the one that also damages normal stem cells
467. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q13164 (MK07_HUMAN), human MAPK7, 816 aa

     · UniProt Consortium 2026
     used by MAPK7 (ERK5) - a DOT1L partner on one 1:365 spoke of one atlas pulldown, and a kinase with real leukaemia literature that has never been connected to DOT1L
468. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P31153 (METK2_HUMAN), S-adenosylmethionine synthase isoform type-2

     UniProt Consortium · UniProt 2026
     used by MAT2A - the enzyme that makes the methyl donor, and the one metabolic dependency in this disease with two independent papers and a lymphoid PDX result
469. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
     Age-restricted vulnerability panel: PLK1, AURKA, MAT2A and FFAR2 dependency in KMT2A-rearranged leukaemia lines

     Oncofusion knowledge graph internal analysis · Oncofusion knowledge graph (internal analysis, ana-age-restricted-vulnerability-panel) 2026
     used by MAT2A - the enzyme that makes the methyl donor, and the one metabolic dependency in this disease with two independent papers and a lymphoid PDX result
470. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9UIS9 (MBD1_HUMAN), Methyl-CpG-binding domain protein 1 / CXXC-type zinc finger protein 3

     UniProt Consortium · UniProtKB 2026
     used by MBD1 - one protein with a methyl-CpG reader and three CXXC fingers, only the third of which binds unmethylated CpG, and whose CXXC fails the MLL-AF9 swap
471. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42322117
     Aberrant splicing of MBD1 reshapes the epigenome to drive convergent myeloerythroid defects in MDS.

     Chen HTT, Joshi P, et al. · Blood 2026
     used by MBD1 - one protein with a methyl-CpG reader and three CXXC fingers, only the third of which binds unmethylated CpG, and whose CXXC fails the MLL-AF9 swap
472. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
     DepMap KMT2A-selective dependency scan over 17,728 genes: analyses/depmap-kmt2a-selective-scan-full/results.json, generated 2026-09-19.

     · DepMap via this repository 2026
     used by MBD3 (O95983) - the methyl-CpG-binding subunit that does NOT bind methylated DNA, and a validated KMT2A::AFF1-selective CRISPR vulnerability that is absent from every column of the pan-fusion interactome
473. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     NCBI esearch via scripts/pubmed_safe.py on 2026-09-24. MBD3[tiab] AND KMT2A[tiab] -> 1 (translation "MBD3"[Title/Abstract] AND "KMT2A"[Title/Abstract], PMID 37686014). MBD3[tiab] AND MLL[tiab] -> 0. MBD3[tiab] AND leukemia[tiab] -> 7. Positive control MEN1[tiab] AND MLL[tiab] -> 55.

     · NCBI PubMed E-utilities 2026
     used by MBD3 (O95983) - the methyl-CpG-binding subunit that does NOT bind methylated DNA, and a validated KMT2A::AFF1-selective CRISPR vulnerability that is absent from every column of the pan-fusion interactome
474. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q05BQ5 (MBTD1_HUMAN); HGNC:19866 (mbt domain containing 1); Ensembl ENSG00000011258

     · UniProt / HGNC / Ensembl 2026
     used by MBTD1 - the H4K20me1/me2 reader inside NuA4/TIP60, the quiescence brake on adult haematopoietic stem cells, and the 3' partner of ZMYND11::MBTD1 whose methyl-lysine cage the fusion carries and does not use, MBTD1 is the effector-recruiting half of a leukaemia fusion and the addressing half of a sarcoma fusion while donating nearly all of itself to both - so the junction, not the parts, assigns the role, MBTD1::EZHIP (MBTD1-CXorf67), t(X;17)(p11.2;q21.33) - MBTD1's other fusion, in which a NuA4 subunit delivers an H3K27M-mimicking PRC2 poison to low-grade endometrial stromal sarcoma, ZMYND11::MBTD1, t(10;17)(p15;q21) - a chromatin reader welded to the NuA4/TIP60 acetyltransferase, maintaining Hoxa/Meis1/Myb/Myc/Sox4 in AML: the KMT2A-fusion architecture built from different parts
475. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     RCSB PDB entry 6NFX and polymer entity 6NFX_1 (rcsb_polymer_entity.pdbx_description; reference_sequence_identifiers Q05BQ5 and Q9H2F5); PDB entries 3FEO and 4C5I

     · RCSB Protein Data Bank 2026
     used by MBTD1 - the H4K20me1/me2 reader inside NuA4/TIP60, the quiescence brake on adult haematopoietic stem cells, and the 3' partner of ZMYND11::MBTD1 whose methyl-lysine cage the fusion carries and does not use
476. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI E-utilities esearch db=pubmed via scripts/pubmed_safe.py, 2026-09-23. querytranslations read back from the responses: "MBTD1"[Title/Abstract] AND "CXorf67"[Title/Abstract]; "MBTD1"[Title/Abstract] AND "EZHIP"[Title/Abstract]; "MBTD1"[Title/Abstract] AND "sarcoma"[Title/Abstract]; "MBTD1"[Title/Abstract] AND "H3K27me3"[Title/Abstract]. Counts and id lists persisted to analyses/q123-the-architecture-from-other-parts-analogy/bounded-searches.json

     · NCBI PubMed 2026
     used by MBTD1 is the effector-recruiting half of a leukaemia fusion and the addressing half of a sarcoma fusion while donating nearly all of itself to both - so the junction, not the parts, assigns the role, MBTD1::EZHIP (MBTD1-CXorf67), t(X;17)(p11.2;q21.33) - MBTD1's other fusion, in which a NuA4 subunit delivers an H3K27M-mimicking PRC2 poison to low-grade endometrial stromal sarcoma
477. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     HGNC:33738 (EZHIP, 'EZH inhibitory protein') and UniProtKB Q86X51 (EZHIP_HUMAN)

     · HGNC / UniProt 2026
     used by MBTD1::EZHIP (MBTD1-CXorf67), t(X;17)(p11.2;q21.33) - MBTD1's other fusion, in which a NuA4 subunit delivers an H3K27M-mimicking PRC2 poison to low-grade endometrial stromal sarcoma, The coverage checker the standing brief mandates overwrites its own HGNC index mid-loop, so every symbol after the first no-match is answered wrongly - and the wrong answer is 'treat any answer as unsafe'
478. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42237892
     The myeloid cell leukaemia-1 inhibitor MIK665 is a potent therapy in preclinical models of paediatric acute myeloid leukaemia.

     Connerty P, Colgan JN, El-Najjar F, ..., Lock RB · Br J Haematol 2026
     used by MCL1 - named in 34 entries of this graph with no entry of its own until now; a mitochondrial survival protein high in infant KMT2A-rearranged ALL, druggable, and so far undruggable in patients
479. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42120360
     MCL1 inhibition to enhance the efficacy of MYB targeting in pediatric acute myeloid leukemia.

     Tsakaneli A, Che N, Virely C, ..., Williams O · Cell Death Dis 2026
     used by MCL1 - named in 34 entries of this graph with no entry of its own until now; a mitochondrial survival protein high in infant KMT2A-rearranged ALL, druggable, and so far undruggable in patients
480. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q07820 (MCL1_HUMAN), Induced myeloid leukemia cell differentiation protein Mcl-1

     UniProt Consortium · UniProt 2026
     used by MCL1 - named in 34 entries of this graph with no entry of its own until now; a mitochondrial survival protein high in infant KMT2A-rearranged ALL, druggable, and so far undruggable in patients
481. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q9HAF1 (EAF6_HUMAN): reviewed record, length, gene names and subcellular-location comments

     UniProt Consortium · UniProtKB/Swiss-Prot 2026
     used by MEAF6 - a 191-residue subunit shared between the NuA4/TIP60 and MOZ/MORF acetyltransferase complexes, whose only two UniProt localisations both cite papers that are not localisation studies
482. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     HGNC record for MEAF6 (HGNC:25674)

     HUGO Gene Nomenclature Committee · HGNC REST 2026
     used by MEAF6 - a 191-residue subunit shared between the NuA4/TIP60 and MOZ/MORF acetyltransferase complexes, whose only two UniProt localisations both cite papers that are not localisation studies
483. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed esearch counts, querytranslations and warninglists for all four H3R2/H4R3 dimethyl states against KMT2A, MLL, the fusion names, menin and revumenib, run twice 2026-09-22

     · NCBI PubMed 2026
     used by Measure H3R2 and H4R3 methylation states at KMT2A-fusion targets by isomer-resolving mass spectrometry, and test the gate by writer perturbation read out on the enzyme's product - the experiment that has never been done in any fusion
484. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted-absence search for replication-dynamics assays in KMT2A-rearranged leukaemia, run 2026-09-20 and title-checked

     · PubMed (NCBI) 2026
     used by Measure replication stress directly in KMT2A-rearranged cells instead of inferring it from a dependency ranking, Transcription–replication conflict as the candidate reason KMT2A-rearranged cells need the Fanconi pathway — a chain with two measured links and three inferred ones
485. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB canonical sequences Q03164 (KMT2A, 3969 aa) and Q9UMN6 (KMT2B, 2715 aa), fetched 2026-09-20

     UniProt Consortium; sequences fetched and aligned by this project · Database 2026
     used by Measure the menin-KMT2B affinity nobody has measured, and the four clinical inhibitors' IC50 against it, Menin holds KMT2A and KMT2B, and the graph has been written as if it held one
486. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.analysis
     analyses/the-eviction-clause-was-reachable-all-along/run.py and results.json plus the input extension, this repository; bins from C:/Temp/q117, C:/Temp/q124 and C:/Temp/q125, computed 2026-09-23 with zero downloads; FLAG series is GSM8123407-412, mislabelled in GEO as H2AK119ub rep1

     Oncofusion knowledge graph, coordinator · internal analysis, reproducible from the repository 2026
     used by Measured against a technical floor of 4-10% from two independent input pairs, PCGF1 loss lowers baseline fusion occupancy at the top-FLAG sites by 16.3% and changes the DOT1L inhibitor's effect on that occupancy by 22.8% - while leaving the menin inhibitor's effect unchanged at 1.3%. In the knockout SGC0946 displaces more fusion than VTP-50469 does, which is the opposite of the control, PCGF1 loss flattens the fusion's genomic distribution - the knockout-over-control share ratio rises monotonically from 0.810 at the highest-signal decile to 1.136 at the lowest while both input pairs stay flat - and the drug does something spatially different: VTP-50469 evicts almost only at the top 0.1% (0.7554 against 0.9937 at the decile below). The drug acts at the peaks, the genotype acts in the bulk, Salvaged from a session-limit death: the DMSO-versus-DMSO selection control cannot be run cleanly on GSE260742, because every same-condition vehicle pair is confounded - two differ about three-fold in aggregate signal and the only admissible same-mark pair crosses processing states (filt.bam.tdf versus tdf). Its automated verdict of MANUFACTURED is NOT supported, and the control remains UNRUN rather than passed or failed, Six files titled H2AK119ub rep1 are FLAG ChIPs, so prediction 5's eviction clause - declared UNREACHABLE by Q124 - was computable from bins already on disk. It is now scored and it CONFIRMS: VTP-50469 removes the same share of fusion occupancy in the PCGF1 knockout as in the control, 0.7655 against 0.7554, a 1.3% difference against 22.8% genotype variation on a control drug, The first measurement of any histone mark outside the top 0.1% of fusion sites: by ratio the drug's mark response is confined to the peaks as pre-registered, while in ABSOLUTE share the movement at the decile below is 5 to 33 times larger - though that is partly guaranteed by the stratum being 100x bigger. H3K79me2 falls at the peaks (0.8065) and is not measurably changed at D1, and H3K4me3 and H3K79me2 both break the floor at the lowest decile, Three unnamed things at once: the DOT1L-PRC1.1 deposition names the fusion, the cell types and both inhibitors with concentrations
487. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     ENCODE CTCF ChIP-seq, conservative IDR thresholded peaks and fold-change-over-control signal, GRCh38: ENCSR000EGM/ENCFF041ODC/ENCFF682MFJ (K562), ENCSR000DZN/ENCFF796WRU/ENCFF485CGE (GM12878), ENCSR000BNH/ENCFF497ZGV/ENCFF038RVZ (H1), ENCSR000AOA/ENCFF533TKY/ENCFF179RSE (HeLa-S3), ENCSR000DLS/ENCFF695QSJ/ENCFF579BUC (HepG2), ENCSR000DTO/ENCFF850PKJ/ENCFF388PVO (HCT116) - all fetched, md5-verified and read this session

     ENCODE Project Consortium · ENCODE Portal 2026
     used by Measured in six ENCODE cell types against every conservative-IDR CTCF anchor of the same cell: the KMT2A exon-11 anchor sits at the 70.6th percentile of CTCF occupancy (range 28.2-81.8, fold over the anchor median 0.69-2.37) - a called peak in 6 of 6 cells and an ORDINARY one, which fails the instrument control the corpus pre-registration wrote for this very experiment
488. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
     analyses/is-any-pi-axis-actually-thin/run.py and results.json, this repository, computed 2026-09-23 over the committed node files; motivated by the Q137 analogy beat's correction of the cycle-113 beat selection

     Oncofusion knowledge graph, coordinator · internal analysis, reproducible from the repository 2026
     used by Measuring every PI-named axis structurally and by content: the type fields understate coverage by a median of 19.5x and by up to 81x, no axis falls below 18% of the corpus, and 'which axis is thinnest' is retired as a beat selector because it reports a lower bound as though it were the truth
489. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed E-utilities esearch record counts for the Mediator subunits MED1, MED12, MED14, MED23 and MED24 against KMT2A, MLL and leukaemia, run for interactome round 5

     · NCBI PubMed, queried 2026-09-19 2026
     used by MED12 - a named menin-associated protein that restrains menin's transcriptional output, and the anchor of the CDK8 module a KMT2A-r AML paper co-targets, MED23 — rank 16 of 17,728, survives the lineage split with the B-lineage half stronger, and is not absent from the leukaemia literature after all
490. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q93074 (MED12_HUMAN), Mediator of RNA polymerase II transcription subunit 12

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by MED12 - a named menin-associated protein that restrains menin's transcriptional output, and the anchor of the CDK8 module a KMT2A-r AML paper co-targets
491. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     IntAct REST findInteractions: interactor EBI-2620048, interaction EBI-4321349 / IMEx IM-16559-13, experimentalRoleA=bait, hostOrganism=Homo sapiens HeLa, retrieved 2026-09-22

     · IntAct molecular interaction database (EMBL-EBI) 2026
     used by MED19 - the Mediator subunit curated against an engineered MLL-AFF4 fusion protein, and the one REST uses to deliver G9a
492. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB A0JLT2 (MED19_HUMAN): features, comments and evidence codes; HGNC:29600 via rest.genenames.org; Ensembl ENSG00000156603 coordinates; retrieved 2026-09-22

     · UniProt Consortium / HGNC / Ensembl 2026
     used by MED19 - the Mediator subunit curated against an engineered MLL-AFF4 fusion protein, and the one REST uses to deliver G9a
493. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
     analyses/depmap-kmt2a-selective-scan-full/results.json - 17,728 protein-coding genes, 11 Cellosaurus-annotated KMT2A-rearranged versus 43 other leukaemia lines, computed 2026-09-19

     · DepMap (Broad Institute), via this repository's scan 2026
     used by MED19 - the Mediator subunit curated against an engineered MLL-AFF4 fusion protein, and the one REST uses to deliver G9a
494. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
     analyses/mediator-module-split/result.json - membership from EBI Complex Portal human table CPX-3227 / CPX-3232 / CPX-3263

     · This repository / EBI Complex Portal 2026
     used by MED19 - the Mediator subunit curated against an engineered MLL-AFF4 fusion protein, and the one REST uses to deliver G9a
495. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     NCBI E-utilities esearch, db=pubmed, querytranslation read back from every response, run 2026-09-22

     · NCBI PubMed 2026
     used by MED19 - the Mediator subunit curated against an engineered MLL-AFF4 fusion protein, and the one REST uses to deliver G9a
496. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9ULK4 (MED23_HUMAN), Mediator of RNA polymerase II transcription subunit 23

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by MED23 — rank 16 of 17,728, survives the lineage split with the B-lineage half stronger, and is not absent from the leukaemia literature after all
497. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted-absence search for MED23 and its aliases against KMT2A/MLL and against leukaemia, run 2026-09-20 and title-checked

     · PubMed (NCBI) 2026
     used by MED23 confirmed, and the zero-record claim corrected: it is not literature-free in leukaemia, an shRNA screen already found it
498. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q9ULK4 (MED23)

     · UniProtKB/Swiss-Prot 2026
     used by MED23 confirmed, and the zero-record claim corrected: it is not literature-free in leukaemia, an shRNA screen already found it
499. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     RCSB PDB entries 5ODD, 6ZV3, 7ENA, 7ENC, 7EMF, 7ENJ, 8GXQ and 8GXS, with per-entity UniProt accessions, methods and modelled residue ranges resolved against the RCSB APIs; searched for MED26 (O95402) complexes with partner peptides

     RCSB Protein Data Bank · RCSB PDB 2026
     used by MED26 — a common-essential Mediator subunit with a solved 87-residue domain and no ChEMBL target entity at all
500. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     ChEMBL database version 34: target_search for MED26 / Mediator complex subunit 26 returned no target entity; comparator targets CHEMBL3232684, CHEMBL3132741, CHEMBL4295801 and CHEMBL4295761 queried by target_search and get_bioactivity

     EMBL-EBI ChEMBL · ChEMBL 2026
     used by MED26 — a common-essential Mediator subunit with a solved 87-residue domain and no ChEMBL target entity at all, VTP-50469 - the preclinical menin-KMT2A interface inhibitor that almost every chromatin experiment in this field actually used, and which had no entry of its own in this graph, ZFP64 — rank 4 on selectivity, and there is not even a ChEMBL entry for it
501. speculative confidence 1 of 5: Our own inference or analogy. Not shown to be true.database
     RCSB PDB entries 5ODD, 6ZV3, 7ENA, 7ENC, 7EMF, 7ENJ, 8GXQ and 8GXS — cited here for the structural facts only; the functional switch interpretation is this project's inference and is not supported by these entries

     RCSB Protein Data Bank · RCSB PDB 2026
     used by MED26 — a common-essential Mediator subunit with a solved 87-residue domain and no ChEMBL target entity at all
502. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O95402 (MED26_HUMAN) - SUBCELLULAR LOCATION comment block with evidence codes

     · UniProt Consortium 2026
     used by MED26 — a common-essential Mediator subunit with a solved 87-residue domain and no ChEMBL target entity at all
503. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
     Core Mediator against its CDK8 kinase module, subunit by subunit, with pan-essentiality and expression controls

     · Oncofusion knowledge graph (internal analysis) 2026
     used by Mediator's KMT2A signal is in its pan-essential core, CDK8 is expressed and not required at all, and MED13L is rank 9 while its paralogue MED13 is rank 13,569
504. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
     Expression control for the paralogue splits and the ALAS1/ALAS2 comparison, against Human Protein Atlas cell-line RNA

     · Oncofusion knowledge graph (internal analysis) 2026
     used by Mediator's KMT2A signal is in its pan-essential core, CDK8 is expressed and not required at all, and MED13L is rank 9 while its paralogue MED13 is rank 13,569, The paralogue split survives the expression control and the ALAS2 control does not: ING4 is transcribed MORE than ING5 and is not required at all
505. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     RCSB PDB structure search against UniProt accession Q06413 (zero results) and UniProtKB Q06413 cross-references, both retrieved via their REST APIs

     RCSB Protein Data Bank; UniProt Consortium · Databases 2026
     used by MEF2C — an output-program transcription factor, the second-strongest leukemia co-dependency, and a gene humans cannot spare one copy of
506. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q06413 (MEF2C_HUMAN) and InterPro/Pfam domain assignments, retrieved via the UniProt and InterPro REST APIs

     UniProt Consortium; InterPro · Databases 2026
     used by MEF2C — an output-program transcription factor, the second-strongest leukemia co-dependency, and a gene humans cannot spare one copy of
507. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O00470 (MEIS1_HUMAN), retrieved via the UniProt REST API

     UniProt Consortium · UniProtKB 2026
     used by MEIS1 — rate-limiting for MLL leukemia stem cells, a surviving co-dependency, and embryonic-lethal when removed
508. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     RCSB PDB entries 4XRS and 5EGO, verified against the RCSB data API for title, experimental method and resolution

     RCSB Protein Data Bank · RCSB PDB 2026
     used by MEIS1 — rate-limiting for MLL leukemia stem cells, a surviving co-dependency, and embryonic-lethal when removed
509. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O00470 (MEIS1_HUMAN) - subcellular location with evidence codes, fetched 2026-09-20

     UniProt Consortium · UniProtKB 2026
     used by MEIS1's 'nucleus' is a profile prediction, not a measurement - and a homeodomain-less isoform is cytoplasmic and does the opposite job
510. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 42441717
     Meis1 isoform diversity orchestrates neural progenitor differentiation by regulating ATOH1 degradation at distinct subcellular compartments.

     Owa T, Adachi T, Shiraishi R, Ichijo K, Ji K, Mizuno M, Suyama K, Nishitani K, Hasegawa I, Sone M, Kawauchi D, Nishioka T · PLoS Biol 2026
     used by MEIS1's 'nucleus' is a profile prediction, not a measurement - and a homeodomain-less isoform is cytoplasmic and does the opposite job
511. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     REVUFORJ (revumenib) and KOMZIFTI (ziftomenib) US prescribing information, retrieved via the openFDA drug label API

     US Food and Drug Administration · openFDA 2026
     used by MEN1 / menin — the adaptor the fusion cannot work without
512. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry O00255 (MEN1_HUMAN), SUBCELLULAR LOCATION comment and feature table

     UniProt Consortium · UniProtKB 2026
     used by MEN1 / menin — the adaptor the fusion cannot work without, Menin residue numbers: the resistance literature (G331R) and the crystal structures (residue 326) disagree by exactly five, Menin's two nuclear localisation signals, 479-497 and 588-608: mapped in 1998, verified residue-for-residue today, annotated by UniProt nowhere - NLS-1 in no structure at all, NLS-2 resolved in one, The menin-gamma-H2A.X motif, menin Val371-Gln400: necessary, sufficient as a peptide, and the nine residues at its centre have never been seen in any of the 69 menin structures, The residue-type numbering check passed a site that is in the wrong place, The ten reported menin-inhibitor escape substitutions are each one nucleotide change from the MEN1 sequence - which the sources could not have shown otherwise - so the useful outputs are a 25-variant validation panel and a burden threshold, not the headline, Three of menin's nine declined partners are E3 ligase substrate receptors - either menin turnover is ubiquitin-controlled, or substrate receptors are this beat's artefact signature, UniProt's menin 214-390 FANCD2 region is not a surface: it spans three spatial lobes and 29.9% of menin's solvent-accessible area, so its twenty-residue overlap with the gamma-H2A.X motif is what chance gives you
513. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 42103719
     CRISPR base editor screening identifies spectrum of MEN1 mutations impacting menin inhibitors in clinical trials

     Bourgeois W, ..., Armstrong SA · Nature Communications 2026
     used by MEN1 drug-interface mutations — the first proof that a chromatin drug can drive Darwinian escape in patients, Model: resistance-mutation prediction - cannot be trained. There are six patient-observed labels in the world, and a base-editor screen already does the job better, Switching menin inhibitors: four substitutions defeat all of them, three defeat only some, and the map now exists, The ten reported menin-inhibitor escape substitutions are each one nucleotide change from the MEN1 sequence - which the sources could not have shown otherwise - so the useful outputs are a 25-variant validation panel and a burden threshold, not the headline
514. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P31749, subcellular location and tissue specificity, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by MEN1-AKT1 is ONE BRET well from a mutation screen, for the E17K allele only - declined
515. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P15056, subcellular location and tissue specificity, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by MEN1-BRAF V600E: four methods and an endogenous menin lane - the only one of the nine that is a real observation, and it is still a property of the allele
516. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q15762, subcellular location and tissue specificity, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by MEN1-CD226 is two proteome-scale AP-MS maps, both spoke-expanded, both in cell lines that do not express CD226 - declined
517. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P00533, subcellular location and tissue specificity, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by MEN1-EGFR is ONE BRET well from the extended-driver arm of a mutation screen, for L858R only - declined
518. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q8N2W9, subcellular location, length and tissue specificity, retrieved 2026-09-24

     · UniProt Consortium 2026
     used by MEN1-PIAS4 - DECLINED. The single supporting publication is a PARP-1 heat-shock sumoylation study in which menin is never named, and the row is a HeLa co-IP passenger
519. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P60484, subcellular location and tissue specificity, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by MEN1-PTEN is ONE BRET well from the extended-driver arm, for R173C only - declined
520. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q13485, subcellular location and tissue specificity, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by MEN1-SMAD4 is four alleles of ONE BRET assay, all 'mutation with no effect' - declined, and the real menin-TGF-beta literature is elsewhere
521. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry O43791, subcellular location and tissue specificity, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by MEN1-SPOP is four alleles of ONE BRET assay, all 'mutation with no effect' - declined, with a nuclear-speckle confound
522. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q86WB0, subcellular location and tissue specificity, retrieved 2026-09-23

     · UniProt Consortium 2026
     used by MEN1-ZC3HC1 is one spoke-expanded BioPlex row in HCT116, and UniProt records ZC3HC1 weakly or not expressed in leukocytes - declined
523. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Cellosaurus search `var:PICALM AND dr:DepMap` and `var:MLLT10 AND dr:DepMap`, gene-fusion records for U-937 (CVCL_0007 / ACH-000406) and TUR (ACH-002314)

     · Cellosaurus / SIB 2026
     used by MEN1, DOT1L and LEDGF dependency in the only CALM-AF10 cell line DepMap has screened
524. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O00255 (MEN1_HUMAN) fetched live from rest.uniprot.org on 2026-09-24 by Q192; each of the fourteen positions indexed into the returned sequence string and the residue printed and compared against the published mutation nomenclature; 14 of 14 matched

     · UniProt Consortium / this repository 2026
     used by Menin binds RPA2 directly, the contact maps to RPA2 aa 43-171 across its low-affinity ssDNA site, and three MEN1 patient missense mutations abolish it - a 2003 finding that this graph had never cited despite menin being its central node, RPA2 (RPA32) - the middle subunit of replication protein A, whose disordered N-terminus is the phospho-switch of the replication-stress response and whose 43-171 region binds menin
525. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P15927 feature table (DNA binding, OB, residues 74-148), fetched live 2026-09-24; and Fan J, Pavletich NP, 'Structure and conformational change of a replication protein A heterotrimer bound to ssDNA', Genes Dev 2012;26(20):2337-47, PMID 23070815, DOI 10.1101/gad.194787.112

     · UniProt Consortium; Genes & Development 2026
     used by Menin binds RPA2 directly, the contact maps to RPA2 aa 43-171 across its low-affinity ssDNA site, and three MEN1 patient missense mutations abolish it - a 2003 finding that this graph had never cited despite menin being its central node, RPA2 (RPA32) - the middle subunit of replication protein A, whose disordered N-terminus is the phospho-switch of the replication-stress response and whose 43-171 region binds menin, RPA2 is the only compartment-compatible candidate of the six and the corpus already has a KMT2A resection thread it would fit — but it is an abundant ssDNA-binding subunit on 6 spectra in a benzonase-treated lysate with no RPA1 or RPA3 co-recovered — declined, thread flagged, Where RPA actually is: nucleoplasmic and diffuse until there is single-stranded DNA, then punctate prereplication foci at the G1/S border, damage-induced foci with RAD51, and a PML-body pool - and the subunits differ in how well any of this is measured
526. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.dataset
     Oncofusion knowledge graph entry ana-reanalysis-of-ml2-mll1n-chip-for-gained-peaks-under-vtp-50469, evidence E3

     · Iqbal Lab oncofusion knowledge graph 2026
     used by Menin inhibition removes the fusion from its strongest sites without relocating it to a new programme, and PRC1.1 fills in only where the eviction is complete - so the drug's chromatin action is subtraction plus local substitution, not redistribution, The falsifier that decides the beat, run: 65.6% of the fusion's own top sites overlap a CpG island and 1 of the 52 sites it formally 'gains' under a menin inhibitor does - 1.35-fold over a class-matched null, Fisher p = 0.53 - so the gained set does not carry the signature of CXXC-driven binding and the redistribution model is refuted on its own predicted substrate
527. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     IntAct REST findInteractions/25962847 (Cheng et al. 2015), 12 records, figure-legend annotated, fetched 2026-09-21

     · EMBL-EBI IntAct 2026
     used by Menin is a corepressor of the LXR sterol sensors - one paper supplies three of this graph's twelve missing partners, and the function has never been written down here, NR1H2 / LXR-beta - the paralogue arm of the menin-LXR contact, present in both species and absent from the paper's conclusion, NR1H3 / LXR-alpha - the best-observed of the three MEN1 sterol partners, with both directions curated in two species, and menin as its corepressor, SREBF1 / SREBP-1 - the weakest of the three MEN1 sterol partners, because it is simultaneously the pathway's readout
528. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     PubMed esearch: menin[tiab] AND (LXR OR "liver X receptor" OR NR1H3 OR NR1H2)[tiab] = 3; menin[tiab] AND (lipogenesis OR steatosis OR SREBP OR "lipid metabolism")[tiab] = 8; menin[tiab] = 1264; run 2026-09-21

     · NCBI PubMed 2026
     used by Menin is a corepressor of the LXR sterol sensors - one paper supplies three of this graph's twelve missing partners, and the function has never been written down here
529. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProt PDB cross-references for O00255, Q03164 and O75475 intersected, with RCSB PDB entry and polymer-entity records for 3U88 read back entity by entity, fetched 2026-09-21

     · RCSB Protein Data Bank / UniProtKB 2026
     used by Menin is the best-observed of the six core proteins and the only one whose interval separates from the rest - the interface the programme is built on is the one the record actually supports
530. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     IntAct REST record EBI-1801742 for the MEN1-PSIP1 pair, fetched 2026-09-21

     · EMBL-EBI IntAct 2026
     used by Menin is the best-observed of the six core proteins and the only one whose interval separates from the rest - the interface the programme is built on is the one the record actually supports, PSIP1-FOXK2: a single TAP row from the same TF atlas as the RBPJ decline - kept as a lead rather than declined, because FOXK2 is a chromatin-recruiting forkhead expressed in lymphoid cells and LEDGF is a chromatin-recruiting tether, PSIP1-RBPJ - DECLINED. A 214-purification transcription-factor TAP atlas that this beat's own atlas heuristic failed to flag, and the Notch connection is the reason to say so out loud, PSIP1-SDC1 - DECLINED as an interaction, kept for the splicing thread: nuclear syndecan-1 co-IP in a mesothelioma line recovers LEDGF among an RNA-splicing-enriched network, RBBP8 / CtIP - the only unwritten core-complex partner with a DIRECT-interaction record, and the graph already held its mechanism without holding the protein, What a curated interaction row actually claims: spoke expansion, and the ladder from 'was in the same tube' to 'touches'
531. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted-absence search for menin and NF-kappaB, with and without a leukaemia term, run 2026-09-20 and title-checked

     · PubMed (NCBI) 2026
     used by Menin represses NF-kB transactivation — through a mapped central region, a SIRT1 cofactor, and an RPA2 off-switch, in every tissue except the one this project cares about
532. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     RCSB PDB entries 9C4S (menin G331R with MLL peptide) and 4GQ6 (wild-type menin with MLL peptide)

     · RCSB PDB 2026
     used by Menin residue numbers: the resistance literature (G331R) and the crystal structures (residue 326) disagree by exactly five
533. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     analyses/q36-menin-residue-axis/run.py - lobe assignment and ligand footprints on PDB 3U84, 7UJ4, 8VA6, 9WKU, 8IG0 and 4GQ6, run 2026-09-22

     · RCSB PDB, computed 2026
     used by Menin stimulates homology-directed repair through Chk1 and the region required is 1-228: a 2010 paper that is cited in no entry of this graph and in no reference list of the 2026 paper that reports the same conclusion, The menin-inhibitor class splits at Val371: three of four clinical compounds contact the first residue of the gamma-H2A.X motif and bleximenib does not, so DNA-repair effects should separate from KMT2A-displacement effects within the class
534. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     PubMed E-utilities esearch via scripts/pubmed_safe.py, query translations read back, 2026-09-22

     · NCBI PubMed 2026
     used by Menin stimulates homology-directed repair through Chk1 and the region required is 1-228: a 2010 paper that is cited in no entry of this graph and in no reference list of the 2026 paper that reports the same conclusion
535. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.analysis
     zhou-group-function-scan: GO:BP enrichment of each menin/H2AK119ub group against Zhou's own called set as custom background, g:Profiler g:SCS corrected

     · Oncofusion knowledge graph (internal analysis) 2026
     used by Menin-bound genes are the RNA-processing and DNA-repair machinery, H2AK119ub-only genes are neuronal and developmental, and 'menin target' is therefore a much weaker label than this graph treats it as
536. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.analysis
     zhou-group-function-scan results: bivalent group GO:BP terms and corrected p-values

     · Oncofusion knowledge graph (internal analysis) 2026
     used by Menin-bound genes are the RNA-processing and DNA-repair machinery, H2AK119ub-only genes are neuronal and developmental, and 'menin target' is therefore a much weaker label than this graph treats it as
537. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset
     analyses/q34-menin-surface-geometry/run.py - menin surface geometry over all 69 O00255 PDB deposits

     Q34-menin-surface-map · Oncofusion Knowledge Graph 2026
     used by Menin-SETD2, mapped to the NTD and Palm and tooled with a peptide at menin 231-248: the third partner assigned to the same half of menin, and the writer arm of the HR scaffold
538. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset
     analyses/q34-menin-surface-geometry/run.py - menin surface geometry over all 69 O00255 PDB deposits

     Q34-menin-surface-map · Oncofusion Knowledge Graph 2026
     used by Menin's nucleosome grip (8GPN): a three-patch surface at menin 353-362, 428-442 and 556-587 that holds H3, H4 and H2B - and touches H2A at exactly one residue, The SvID, menin 360-445: a truncation boundary the field reads as a domain, whose functional residues D418 and W436 are 10-20 A from every menin drug - but whose first ten residues ARE the drug pocket
539. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.computation_on_public_coordinates
     Observed-residue survey of all 69 menin (UniProt O00255) PDB deposits, with a residue-identity guard against non-corresponding deposited numbering

     king, Oncofusion knowledge graph, cycle 64 · analyses/menin-nls-structural-coverage/run.py 2026
     used by Menin's two nuclear localisation signals, 479-497 and 588-608: mapped in 1998, verified residue-for-residue today, annotated by UniProt nowhere - NLS-1 in no structure at all, NLS-2 resolved in one
540. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9HCE5 (MET14_HUMAN), human METTL14, 456 aa

     · UniProt Consortium 2026
     used by METTL14 — the other half of the m6A writer, with a real AML mechanism and zero KMT2A-specific records
541. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q86U44 (MTA70_HUMAN), human METTL3, 580 aa

     · UniProt Consortium 2026
     used by METTL3 — the m6A writer with a clinical-grade inhibitor, an MLL-rearranged AML mechanism, and a B-lymphoid signal that goes the wrong way
542. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     HGNC REST API record for MIR196B and Ensembl REST API gene lookups (MIR196B, HOXA9, HOXA10), assembly GRCh38

     HUGO Gene Nomenclature Committee; Ensembl / EMBL-EBI · HGNC / Ensembl 2026
     used by miR-196b — the HOXA-cluster microRNA that is a direct KMT2A-fusion target and a genuine double agent
543. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     HGNC REST API records for MIR9-1, MIR9-2, MIR9-3 and Ensembl REST API gene lookups (MIR9-1/2/3, MEF2C), assembly GRCh38

     HUGO Gene Nomenclature Committee; Ensembl / EMBL-EBI · HGNC / Ensembl 2026
     used by miR-9 — the most MLL-specific microRNA in AML, encoded at three separate loci nobody has disambiguated
544. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed database queries 'miR-9 AND MLL AND leukemia' (4 records) and 'miR-9 AND KMT2A AND rearranged AND leukemia' (0 records), executed 2026-09-18

     National Library of Medicine, PubMed · PubMed 2026
     used by miR-9 — the most MLL-specific microRNA in AML, encoded at three separate loci nobody has disambiguated
545. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paperPMID 41692013
     Bortezomib and vorinostat in combination with mitoxantrone, dexamethasone, and pegasparaginase during induction and reinduction for infants with acute lymphoblastic leukaemia: a multicentre single-arm phase 1/2 study.

     Gruber TA, Jeha S, Deyell RJ, Lewis V, Chang BH, Lowe EJ, et al. · Lancet Haematol 2026
     used by Mitoxantrone - the Interfant-06 protocol says it is less cardiotoxic than daunorubicin, and the largest survivor cohort ever assembled says it is about seventeen times worse per milligram, Native E. coli asparaginase - the second-largest in-vitro resistance signal in infant ALL, and a different product from the pegylated one four doses later, Pegaspargase - the same enzyme wearing a polymer, dosed in units that are not the other product's units, and now dosed to a level in every group except infants, Romidepsin - the HDAC inhibitor with the best preclinical case in KMT2A-rearranged INFANT ALL specifically, and a mechanism that is not about histones at all, Vorinostat (SAHA) - the only HDAC inhibitor given to newly diagnosed infants with ALL, in a 50-patient trial whose endpoint was tolerability and which reported four treatment-related deaths, all infectious
546. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.reviewPMID 41063702
     Acute leukemia of ambiguous lineage: the known and the uncertain

     Sherban A, Wolach O · Haematologica 2026
     used by Mixed-phenotype acute leukemia and KMT2A rearrangement — plasticity caught in the act
547. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     ChEMBL database version 34, target CHEMBL4295801 (Protein ENL): target_search, get_bioactivity and get_mechanism queries

     EMBL-EBI ChEMBL · ChEMBL 2026
     used by MLLT1 / ENL — the reader that beat its own paralogue, with a degrader already in hand
548. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     RCSB PDB entries 5J9S, 6HPW, 6HPX, 6HPY, 6HPZ, 6HT0, 6HT1, 6T1I, 6T1J, 6T1L, 6T1M, 6T1N, 6T1O, 9DUR and 4TMP, with per-entity UniProt accessions, ligands, methods, resolutions and modelled residue ranges resolved against the RCSB search and data GraphQL APIs

     RCSB Protein Data Bank · RCSB PDB 2026
     used by MLLT1 / ENL — the reader that beat its own paralogue, with a degrader already in hand
549. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     ChEMBL database version 34, targets CHEMBL4295761 (Protein AF-9) and CHEMBL4295801 (Protein ENL): target_search, get_bioactivity and get_mechanism queries

     EMBL-EBI ChEMBL · ChEMBL 2026
     used by MLLT3 / AF9 — a famous fusion partner that is not a dependency, and a hub domain that is
550. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P42568 (AF9_HUMAN), SUBCELLULAR LOCATION comment and feature table

     UniProt Consortium · UniProtKB 2026
     used by MLLT3 / AF9 — a famous fusion partner that is not a dependency, and a hub domain that is, The KMT2A::MLLT3 chimeric protein: what survives the join on each side, in residue numbers - and the four AF9 modules that do not, Where KMT2A::MLLT3 sits in the nucleus: two papers, both overexpression, both from before 2005 - and the fusion carries no AF9 import signal
551. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P55198 (AF17_HUMAN) Protein AF-17, Homo sapiens, 1093 aa

     UniProt Consortium · UniProtKB 2026
     used by MLLT6 / AF17 — domain architecture, and where the leucine zipper actually is
552. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P08473 (NEP_HUMAN), Neprilysin, EC 3.4.24.11, common acute lymphocytic leukemia antigen, 750 aa, single reviewed human record, primary gene name MME

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by MME / CD10 (CALLA) - the marker this disease is defined by NOT having, and the promoter is methylated shut rather than simply not yet switched on
553. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42303978
     Detection of MEN1 resistance mutations in cell-free DNA from acute leukemia patients treated with menin inhibitors

     Shukla N, et al. · Blood Cancer Journal 2026
     used by Model: resistance-mutation prediction - cannot be trained. There are six patient-observed labels in the world, and a base-editor screen already does the job better, Switching menin inhibitors: four substitutions defeat all of them, three defeat only some, and the map now exists
554. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Cellosaurus cell line records CVCL_0064 (MV4-11), CVCL_0006 (THP-1), CVCL_1609 (NOMO-1), CVCL_2191 (SHI-1), CVCL_2119 (MOLM-13) and CVCL_7916 (MOLM-14), retrieved via the Cellosaurus API

     Bairoch A; SIB Swiss Institute of Bioinformatics · Cellosaurus 2026
     used by Monocyte — the graph's most-discussed undefined cell identity, and the confound sitting under its own DepMap haem signal, The monocytic confound is worse than recorded: two of the six rearranged lines are one patient, and the four-line control group contains a HOXA-driven fusion and two NPM1c/myelomonocytic lines
555. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.dataset
     Q154 gene-body class membership, margins and threshold sweep

     Iqbal Lab oncofusion knowledge graph, beat Q154 · this project 2026
     used by Most gene-body 'AFF1-exclusive' calls in GSE252378 are a fold-change threshold cutting an oncoprotein-level gradient - and IRX1 is the one member where the non-AFF1 samples are genuinely at background, Six gene bodies are AFF1-exclusive and recurrent at gene scale; the authors' own pipeline confirms one of them, refutes three and has never measured two - and IRX1 is the one it confirms
556. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.reviewPMID 42489798
     Incorporating Immunotherapies into the Evolving Standard of Care for Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia.

     Lissat A, Brivio E, Stutterheim J, et al. · Paediatr Drugs 2026
     used by MRD as a trial endpoint in KMT2A-rearranged leukaemia: high negativity rates, and almost none of them say which assay
557. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     DepMap CRISPR gene-effect (Chronos) for MRE11, served by the Open Targets Platform GraphQL API

     Broad Institute DepMap / Open Targets Platform · Open Targets Platform 26.06 (meta.dataVersion year 26 month 06), fetched 2026-09-22 2026
     used by MRE11 (P49959, 708 aa) - the nuclease that makes the first cut of end resection, named in 10 entries of this graph and never written; DepMap mean -0.542 with 56% of 1,258 lines below -0.5, the deepest dependency in the whole resection cascade
558. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q96DH6 (MSI2H_HUMAN), human MSI2, 328 aa

     · UniProt Consortium 2026
     used by MSI2 (Musashi-2) — sustains the MLL stem-cell programme in mouse, and the myeloid DepMap arm disagrees in sign
559. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q68DK7 (MSL1_HUMAN), Male-specific lethal 1 homolog

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by MSL1 - the MSL scaffold that carries MOF and MSL2 to HOXA9 and MEIS1, with zero records against KMT2A and a mapped, drawable domain architecture
560. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed E-utilities esearch record counts for MSL1 and the MSL complex against KMT2A, MLL and leukaemia, run for interactome round 5

     · NCBI PubMed, queried 2026-09-19 2026
     used by MSL1 - the MSL scaffold that carries MOF and MSL2 to HOXA9 and MEIS1, with zero records against KMT2A and a mapped, drawable domain architecture
561. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     NCBI esearch via scripts/pubmed_safe.py on 2026-09-24. MTA2[tiab] AND KMT2A[tiab] -> 0 (translation "MTA2"[Title/Abstract] AND "KMT2A"[Title/Abstract]). MTA2[tiab] AND MLL[tiab] -> 0. MTA2[tiab] AND leukemia[tiab] -> 2 (PMIDs 23466416, 16091750). MTA1L1[tiab] -> 4 (24055374, 16309230, 12684393, 9929979). MTA2[tiab] AND NuRD[tiab] -> 54. Positive control MEN1[tiab] AND MLL[tiab] -> 55.

     · NCBI PubMed E-utilities 2026
     used by MTA2 / MTA1L1 (O94776) - the NuRD scaffold that clamps HDAC1, recruited in T lymphocytes by BCL11B, and absent together with MTA1 and MTA3 from every column of the pan-MLL-fusion interactome, No experiment has ever ASKED whether MTA2, MBD3, GATAD2A or SIN3A binds a KMT2A fusion - four of them were nonetheless in the lysate of a seven-fusion pulldown, and the class of that absence is measured-not-reported, not never-measured
562. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
     DepMap KMT2A-selective dependency scan over 17,728 genes: analyses/depmap-kmt2a-selective-scan-full/results.json, generated 2026-09-19. MTA2 rank 1,037, difference -0.1047, mean_kmt2a_r -0.3976, mean_other -0.2929, pan_essentiality -0.2103.

     · DepMap via this repository 2026
     used by MTA2 / MTA1L1 (O94776) - the NuRD scaffold that clamps HDAC1, recruited in T lymphocytes by BCL11B, and absent together with MTA1 and MTA3 from every column of the pan-MLL-fusion interactome
563. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P11586 (C1TC_HUMAN), C-1-tetrahydrofolate synthase, cytoplasmic

     UniProt Consortium · UniProt 2026
     used by MTHFD1 (P11586) - the inverse case: the deepest leukaemia dependency in the serine/one-carbon panel, and the drug does not touch it
564. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     NCBI E-utilities esearch against PubMed, 2026-09-22, fusion operand set (KMT2A[tiab] OR MLL[tiab] OR "MLL-AF4"[tiab] OR "KMT2A::AFF1"[tiab] OR "MLL-rearranged"[tiab] OR "t(4;11)"[tiab] OR "MLL-AF9"[tiab] OR "MLL-ENL"[tiab]), each term separately tagged and every cytogenetic term quoted

     · PubMed 2026
     used by MTHFD1 (P11586) - the inverse case: the deepest leukaemia dependency in the serine/one-carbon panel, and the drug does not touch it
565. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P13995 (MTDC_HUMAN), Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial

     UniProt Consortium · UniProt 2026
     used by MTHFD2 (P13995) - the one panel member with a published MLL-AF9 in-vivo survival result, and the serine gene that behaves exactly like an ISR gene
566. weak confidence 2 of 5: Preliminary, small, indirect, or not yet peer reviewed.database
     IntAct molecular interaction database, PSICQUIC MITAB 2.7, query id:Q5JR59 AND id:Q9UHB7, 3 rows retrieved 2026-09-21

     · IntAct (EMBL-EBI) 2026
     used by MTUS2 (TIP150) - a microtubule plus-end tracking protein with 153 partners in the one yeast screen that reported it binding AFF4
567. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry Q5JR59 (MTUS2_HUMAN, Microtubule-associated tumor suppressor candidate 2), subcellular location and function comments with evidence codes

     · UniProtKB/Swiss-Prot 2026
     used by MTUS2 (TIP150) - a microtubule plus-end tracking protein with 153 partners in the one yeast screen that reported it binding AFF4
568. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted-absence search for MTUS2/TIP150 against MLL, KMT2A and leukaemia, run 2026-09-21

     · PubMed (NCBI) 2026
     used by MTUS2 (TIP150) - a microtubule plus-end tracking protein with 153 partners in the one yeast screen that reported it binding AFF4
569. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     Cell Ontology term lookup via the EMBL-EBI Ontology Lookup Service OLS4 API

     EMBL-EBI Ontology Lookup Service; Cell Ontology consortium · Database 2026
     used by Multipotent progenitor (MPP) — the stage where the undifferentiated KMT2A-r infant leukaemias map
570. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P10242 (MYB_HUMAN), Transcriptional activator Myb

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by MYB — rank 17 of 17,728 for KMT2A selectivity, and the only node in this beat where partial, transient suppression eradicated leukaemia without stopping normal blood production
571. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q9BQG0 (MBB1A_HUMAN) and HGNC REST fetch/symbol/MYBBP1A

     2026
     used by MYBBP1A - the let-7-independent effector through which LIN28B suppresses MLL-rearranged AML, and a nucleolar MYB co-repressor that reads H3K9me2
572. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42014858
     HDAC8 inhibition targets STAT3-MYC axis and synergizes with Venetoclax in KMT2A-rearranged acute myeloid leukemia

     Zhang L, ..., Kuo YH · Leukemia 2026
     used by MYC - named in a hundred entries of this graph and, until now, written in none
573. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed human record for MYC, gene_exact:MYC AND organism_id:9606 AND reviewed:true

     · UniProt 2026
     used by MYC - named in a hundred entries of this graph and, until now, written in none
574. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.trial_registry
     A Phase I Study Investigating the Combination of the Menin Inhibitor Ziftomenib With Venetoclax and Gemtuzumab in Pediatric Patients With Acute Myeloid Leukemia

     M.D. Anderson Cancer Center · ClinicalTrials.gov 2026
     used by Myeloid-directed antigens (CD33, CD123) — the only immunotherapy axis that survives lineage switch
575. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P35749 (MYH11_HUMAN): reviewed sequence, length and positional feature annotations

     UniProt Consortium · UniProtKB/Swiss-Prot 2026
     used by MYH11 — domain architecture and residue coordinates
576. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     PDB 9FU2 'Smooth Muscle Myosin II in complex with MT-228' (title retrieved and verified at RCSB; released 2025)

     RCSB Protein Data Bank (entry metadata retrieved and title verified) · RCSB PDB 2026
     used by MYH11 — domain architecture and residue coordinates
577. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     AlphaFold Protein Structure Database entry for P35749 (model AF-P35749-F1)

     Jumper J, Varadi M, et al.; EMBL-EBI/DeepMind · AlphaFold DB 2026
     used by MYH11 — domain architecture and residue coordinates
578. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     PDB 9FU2 'Smooth Muscle Myosin II in complex with MT-228': observed-residue ranges from the RCSB polymer entity instance record for chain A

     RCSB Protein Data Bank (entry and instance metadata retrieved and read back) · RCSB PDB 2026
     used by MYH11 — domain architecture and residue coordinates
579. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     InterPro member-database domain matches for UniProt P35749 (Pfam, PROSITE, SMART, CDD, CATH-Gene3D, SUPERFAMILY)

     InterPro Consortium; EMBL-EBI · InterPro 2026
     used by MYH11 — domain architecture and residue coordinates
580. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted-absence search for MYH9 against KMT2A/MLL/menin, run 2026-09-20, hit title-checked

     · PubMed (NCBI) 2026
     used by MYH9 (non-muscle myosin IIA) — the best-validated menin partner nobody in this field talks about, and the only one that maps to menin's N-terminus
581. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB entry P35579 (MYH9_HUMAN, Myosin-9)

     · UniProtKB/Swiss-Prot 2026
     used by MYH9 (non-muscle myosin IIA) — the best-validated menin partner nobody in this field talks about, and the only one that maps to menin's N-terminus
582. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB O00160 (MYO1F_HUMAN) Unconventional myosin-If, Homo sapiens, 1098 aa

     UniProt Consortium · UniProtKB 2026
     used by MYO1F — unconventional myosin IF, a KMT2A partner with neither a transactivation domain nor a dimerisation domain
583. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P49321 (NASP_HUMAN) and Q99MD9 (NASP_MOUSE), SUBCELLULAR LOCATION comments with evidence codes and sources plus the NLS feature and TISSUE SPECIFICITY, both fetched live 2026-09-21

     UniProt Consortium · Databases 2026
     used by NASP - the soluble histone reservoir, and the only gene in this beat with a real selective difference at a pan-essentiality shallow enough to interpret
584. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paperPMID 42085640
     Toxicity from asparaginase during acute lymphoblastic leukemia induction: a report from the Children's Oncology Group.

     Orgel E, Maese LD, Devidas M, Militano O, Rau RE, Angiolillo AL, et al. · Blood Adv 2026
     used by Native E. coli asparaginase - the second-largest in-vitro resistance signal in infant ALL, and a different product from the pegylated one four doses later
585. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     DepMap CRISPR gene-effect (Chronos) for NBN, served by the Open Targets Platform GraphQL API

     Broad Institute DepMap / Open Targets Platform · Open Targets Platform 26.06 (meta.dataVersion year 26 month 06), fetched 2026-09-22 2026
     used by NBN / nibrin (O60934, 754 aa) - the MRN subunit whose loss causes a leukaemia-predisposition syndrome and yet is almost dispensable in DepMap: mean -0.047 against MRE11's -0.542 in the same complex, the same call and the same release
586. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     TARGET — Therapeutically Applicable Research to Generate Effective Treatments (NCI Center for Cancer Genomics programme page)

     National Cancer Institute, Center for Cancer Genomics / Office of Cancer Genomics · cancer.gov 2026
     used by NCI TARGET — a finished paediatric leukaemia genomics resource, not an active partner
587. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     GDC Projects API query for program.name = TARGET, returning project_id, name, summary.case_count and summary.file_count for all TARGET projects

     NCI Genomic Data Commons · api.gdc.cancer.gov 2026
     used by NCI TARGET — a finished paediatric leukaemia genomics resource, not an active partner
588. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     Using TARGET Data (NCI Center for Cancer Genomics)

     National Cancer Institute, Center for Cancer Genomics · cancer.gov 2026
     used by NCI TARGET — a finished paediatric leukaemia genomics resource, not an active partner
589. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.dataset
     NCBI PubMed E-utilities esearch with querytranslation inspected, and UniProtKB reviewed human record Q14686 (NCOA6); queries run 2026-09-20 by this project

     NCBI PubMed; UniProt Consortium; queries run by this project · Database 2026
     used by NCOA6 (ASC-2) - the subunit that gives MLL3 and MLL4 their target genes, and a recorded near-absence in leukaemia
590. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.trial_registry
     A Phase 1/2 Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics, and Efficacy of SNDX-5613 in Patients With Colorectal Cancer and Other Solid Tumors

     · ClinicalTrials.gov 2026
     used by NCT05631574 (COVALENT-102): the third solid-tumour menin-inhibitor trial, missing from this graph because its drug is called BMF-219 - terminated after 13 patients for a strategic reason, explicitly NOT for efficacy or safety, No menin inhibitor has ever enrolled a KMT2A-rearranged solid tumour, and the one solid-tumour menin trial that read out was terminated for lack of efficacy, The predictable clinical error this beat exists to prevent: a menin inhibitor given for a KMT2A-rearranged sarcoma because of the gene name
591. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.analysis
     Aldehyde versus replication: co-dependency test of the Fanconi ubiquitin-transfer module across 54 leukaemia lines

     · Oncofusion knowledge graph (internal analysis) 2026
     used by Neither rival mechanism leaves its fingerprint, and the best correlate of Fanconi dependency is menin
592. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB records Q9H3P2 (NELFA), Q8WX92 (NELFB), Q8IXH7 (NELFCD) and P18615 (NELFE)

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by NELF — the brake that has to come off for elongation, absent from the KMT2A literature, and less required in KMT2A-rearranged lines than in any other leukaemia, NELFE (RDBP) — the RNA-binding subunit of the pausing brake, and the alias that inflated a record count fifty-fold before it was caught
593. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB Q8WX92 (NELFB_HUMAN), Negative elongation factor B

     · UniProt Knowledgebase, reviewed (Swiss-Prot) 2026
     used by NELFB (COBRA1) — the NELF scaffold, and the single least KMT2A-selective gene of the sixty least selective in the genome
594. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.database
     PubMed E-utilities esearch record counts for NELFE and its aliases against KMT2A and MLL, with and without the two-letter alias RD, run for this beat

     · NCBI PubMed, queried 2026-09-19 2026
     used by NELFE (RDBP) — the RNA-binding subunit of the pausing brake, and the alias that inflated a record count fifty-fold before it was caught
595. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB reviewed human entries retrieved by gene_exact:NF1 and by protein_name:"nuclear factor 1", with fields accession, gene_primary, gene_synonym, protein_name and length

     UniProt Consortium · UniProt 2026
     used by NF1 - the only tumour-suppressor loss in this disease, and it is a deletion, so a mutation panel cannot see it
596. moderate confidence 3 of 5: One strong study, or several smaller consistent ones.paperPMID 42440143
     The clinical relevance of RAS pathway gene mutations in childhood B-cell acute lymphoblastic leukemia.

     Chen X, Gao L, Zhang Y, et al. · Annals of Hematology 2026
     used by NF1 - the only tumour-suppressor loss in this disease, and it is a deletion, so a mutation panel cannot see it, NRAS - the other RAS, the one whose 0.3% clone came back, and a UniProt record that lists HRAS1 as its own synonym, PTPN11/SHP2 - non-recurrent in infant KMT2A-rearranged ALL, well drugged everywhere else, and the one leukaemia trial that carried a SHP2 inhibitor was withdrawn, The RAS-mutant subclone is where the leukaemia goes, not what it is - a dissemination modifier that a marrow aspirate systematically under-counts
597. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P21359 (NF1_HUMAN), SUBCELLULAR LOCATION comments, NLS feature and TISSUE SPECIFICITY, fetched live 2026-09-21

     UniProt Consortium · Databases 2026
     used by NF1 - the only tumour-suppressor loss in this disease, and it is a deletion, so a mutation panel cannot see it
598. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted-absence search for NFKB1 aliases against KMT2A/MLL, run 2026-09-20, every hit title-checked

     · PubMed (NCBI) 2026
     used by NFKB1 (p105/p50) — the only menin-NF-kB subunit with a co-immunoprecipitation, and the arm the MLL leukaemia data points at
599. established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
     UniProtKB P19838 (NFKB1_HUMAN), both molecule-scoped SUBCELLULAR LOCATION comments with evidence codes, sources and notes, plus the NLS feature, fetched live 2026-09-21

     UniProt Consortium · Databases 2026
     used by NFKB1 (p105/p50) — the only menin-NF-kB subunit with a co-immunoprecipitation, and the arm the MLL leukaemia data points at
600. strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.database
     PubMed counted-absence search for NFKB2 aliases against KMT2A/MLL, run 2026-09-20

     · PubMed (NCBI) 2026
     used by NFKB2 (p100/p52) — menin binds the non-canonical subunit too, and activating that arm SUPPRESSES MLL-AF9 leukaemia