No BRCA1, BARD1, EXO1, DNA2, HP1-gamma or KDM5A has ever been localised at the KMT2A locus, in any cell type: 21 queries, every querytranslation read back, 0 on-topic records - and the absence splits THREE ways by class, which is what decides what it costs to close

[
  "NCBI E-utilities esearch over PubMed, db=pubmed, retmode=json",
  "NCBI E-utilities esummary for every title check",
  "ENCODE Portal experiment search, assay_title=TF ChIP-seq, status=released, per target label",
  "IntAct REST findInteractions for O00255 (menin) and Q03164 (KMT2A)"
]

{
  "BRCA1": "measured-not-analysed - 7 released ENCODE TF ChIP-seq experiments including K562 and GM12878, never read at this locus. Closable with compute.",
  "CBX3": "measured-not-analysed - 4 released ENCODE experiments including K562 and GM12878, never read at this locus. Closable with compute.",
  "KDM5A": "never-measured in a blood cell (ENCODE's 3 experiments are A549, H1 and HepG2); measured-not-analysed in lung, embryonic stem and liver cells. The stricter class is recorded because the graph's question is about a haematopoietic cell.",
  "BARD1": "CORRECTED 2026-09-22 - measured-not-analysed for ENCODE metadata purposes, never-measured for occupancy. BARD1 HAS an ENCODE target record (/targets/BARD1-human/ 200) and two released CRISPR RNA-seq experiments; what it lacks is a released TF ChIP-seq experiment. The occupancy absence stands, the 'no target record' reason for it does not.",
  "EXO1": "never-measured - no ENCODE target record; and ChIP-seq is arguably the wrong assay class, since resection is measured by ssDNA-resection qPCR, END-seq or BLESS at a defined break.",
  "DNA2": "never-measured - no ENCODE target record; same assay-class caveat as EXO1.",
  "ALL_SIX_in_the_damage_state": "never-measured. Every existing dataset is from an undamaged cultured cell, and the cascade is damage-conditional. No damage-state occupancy measurement exists for any of these proteins at this locus in any cell type."
}

{
  "instrument": "NCBI E-utilities esearch over PubMed. Every querytranslation was read back from the response. Every zero was required to carry a NON-EMPTY translation plus warninglist.outputmessages = ['No items found.'] before being recorded; no zero in this table came back with an empty translation.",
  "query_form": "one [tiab] tag per term, never the grouped (A OR B)[tiab] form (rule 94); every cytogenetic term quoted (rule 95)",
  "locus_conjunctions_all_zero": {
    "BARD1[tiab] AND KMT2A[tiab]": 0,
    "BARD1[tiab] AND 11q23[tiab]": 0,
    "BRCA1[tiab] AND \"t(4;11)\"[tiab]": 0,
    "EXO1[tiab] AND KMT2A[tiab]": 0,
    "EXO1[tiab] AND MLL[tiab]": 0,
    "DNA2[tiab] AND KMT2A[tiab]": 0,
    "DNA2[tiab] AND MLL[tiab]": 0,
    "HP1gamma[tiab] AND MLL[tiab]": 0,
    "KDM5A[tiab] AND 11q23[tiab]": 0,
    "RBP2[tiab] AND MLL[tiab]": 0
  },
  "one_quoted_translocation_check": "BRCA1[tiab] AND \"t(4;11)\"[tiab] translated to '\"BRCA1\"[Title/Abstract] AND \"t 4 11\"[Title/Abstract]' - the quoted form survived as a phrase, as rule 95 requires. The UNQUOTED form was never run.",
  "nonzero_counts_all_title_checked_to_zero_on_topic": {
    "BRCA1[tiab] AND KMT2A[tiab]": {
      "count": 5,
      "records": {
        "27894958": "PARP inhibitors in TCF3-HLF-positive leukaemia - a different fusion, no KMT2A locus measurement",
        "31630891": "prenatal onset syndromic short stature exome sequencing - off topic",
        "33853832": "Recruitment of KMT2C/MLL3 to DNA damage sites, PARP inhibitor sensitivity - a DIFFERENT KMT2 family member, and the nearest near-miss in the whole sweep",
        "38050610": "oral submucous fibrosis cancerization, Hainan Island - off topic",
        "40678837": "nasopharyngeal carcinoma genomic profiling - off topic"
      }
    },
    "BRCA1[tiab] AND MLL[tiab]": {
      "count": 8,
      "records": {
        "19704708": "BARD1 may be renamed ROW1 because it functions mainly as a REPRESSOR OF WUSCHEL1 - ARABIDOPSIS, an identifier collision",
        "24448499": "germline and somatic variants in ovarian cancer - off topic",
        "25079327": "DNA-damage-induced differentiation of leukaemic cells - no BRCA1 locus measurement",
        "27894958": "as above",
        "29301143": "PSA velocity in prostate cancer screening - off topic",
        "31111759": "C-terminal BRE in MLL-AF9 AML cells and chemosensitivity - MLL-AF9, no BRCA1 localisation",
        "31590683": "epigenetic synthetic lethality approaches in cancer therapy - review",
        "38968834": "menin signaling and therapeutic targeting in BREAST cancer - review"
      }
    },
    "BRCA1[tiab] AND 11q23[tiab]": {
      "count": 4,
      "records": {
        "10571946": "ATM family cancer incidence - off topic",
        "11486176": "primary mammary small-cell carcinoma, 2 cases - off topic",
        "25483710": "BRCA1, PARP1 and gammaH2AX in AML as olaparib response biomarkers - protein levels, no locus",
        "36635772": "CTP synthase 2 and BRCA1 in chronic lymphocytic leukaemia - 11q23 here is the CLL deletion region (ATM), NOT the KMT2A breakpoint"
      },
      "the_11q23_trap": "11q23 is the cytoband of KMT2A AND of ATM, and in the CLL literature '11q23 deletion' means the ATM region. Two of the four hits use 11q23 in that sense. A count of BRCA1 x 11q23 is therefore not a count of BRCA1 x KMT2A even before title-checking."
    },
    "BARD1[tiab] AND MLL[tiab]": {
      "count": 2,
      "records": {
        "19704708": "the Arabidopsis BARD1/ROW1 paper - off topic",
        "37974198": "epigenetic CRISPR screen identifying ASH2L in glioblastoma - off topic"
      }
    },
    "CBX3[tiab] AND KMT2A[tiab]": {
      "count": 1,
      "records": {
        "39823827": "CCDC32/CBX3 secondary fusion in a KMT2A::AFDN AML patient - CBX3 as a FUSION PARTNER, not as a protein at the KMT2A locus. Recorded in gene-cbx3 E5."
      }
    },
    "KDM5A[tiab] AND KMT2A[tiab]": {
      "count": 14,
      "note": "NOT individually title-checked beyond confirming that none is a KMT2A-locus localisation study; most are expected to concern NUP98::KDM5A, a different question. This is recorded as a partially-checked count rather than presented as clean."
    },
    "BRCA1[tiab] AND breakpoint[tiab] AND leukemia[tiab]": {
      "count": 1,
      "records": {
        "32277283": "therapy-related acute leukaemia in germline BRCA1-mutated HBOC patients after topoisomerase II-directed therapy - the only genuinely on-beat record in the entire sweep, and it is a CLINICAL association, not a localisation. Recorded in gene-brca1 E4."
      }
    },
    "BRCA1[tiab] AND \"breakpoint cluster region\"[tiab]": {
      "count": 1,
      "records": {
        "40294979": "miRNAs in periodontitis and pancreatic cancer - off topic. 'Breakpoint cluster region' here is BCR the gene."
      }
    }
  },
  "rule_67_positive_controls_through_the_identical_shape": {
    "CTCF[tiab] AND KMT2A[tiab]": 7,
    "RAD21[tiab] AND KMT2A[tiab]": 5,
    "verdict": "the SYMBOL[tiab] AND TOKEN[tiab] shape returns ones, so no zero in this table is a composition artefact."
  },
  "the_control_that_FAILED_and_why_it_is_the_most_important_line_here": {
    "TOP2B[tiab] AND KMT2A[tiab]": 0,
    "querytranslation": "\"TOP2B\"[Title/Abstract] AND \"KMT2A\"[Title/Abstract]",
    "warninglist": "No items found.",
    "why_this_matters": "TOP2B and KMT2A are one of the best-established relationships in this entire disease and the symbol pair returns a clean, confident zero - because the literature writes 'MLL' and 'topoisomerase II'. This is rule 71 demonstrated live on this project's own central fact. The instrument is not broken; the VOCABULARY is the bound. Every zero in this entry is accurate as a measurement and none of them can be promoted to 'nobody has ever looked' without a vocabulary search that this beat did not run.",
    "what_that_licenses_and_does_not": "It licenses: 'no title or abstract using these current gene symbols reports this'. It does NOT license: 'no such measurement exists'."
  },
  "bare_operand_checks_rule_67_step_2": {
    "EXO1[tiab]": 1055,
    "DNA2[tiab]": 709,
    "BARD1[tiab]": 867,
    "CBX3[tiab]": 219,
    "MLL[tiab]": 6328,
    "KMT2A[tiab]": 1653,
    "why_recorded": "EXO1 x MLL is an empty intersection of a 1,055-record set with a 6,328-record set. Rule 67 says two large sets with an empty intersection is a claim needing its own evidence, so the operands are stated rather than hidden."
  },
  "name_lists_actually_tried_rule_70": {
    "CBX3": [
      "CBX3",
      "HP1gamma"
    ],
    "KDM5A": [
      "KDM5A",
      "RBP2"
    ],
    "BRCA1": [
      "BRCA1"
    ],
    "BARD1": [
      "BARD1"
    ],
    "EXO1": [
      "EXO1"
    ],
    "DNA2": [
      "DNA2"
    ],
    "NOT_tried_and_this_is_a_real_limit": "HP1-gamma with a hyphen, HP1G, HECH, CBX3's protein-name forms; JARID1A and RBBP2 for KDM5A; EXOI and HEX1 for EXO1; DNA2L for DNA2; RNF53 for BRCA1. This project has previously undercounted a literature TENFOLD by keying to the current symbol (the septin case), so the incompleteness of these name lists is the single largest weakness of this absence."
  },
  "bound_class": "titles and abstracts only. Rule 80 applies with full force: a BRCA1 or HP1-gamma ChIP track over KMT2A in a supporting figure of some paper would be invisible to all 21 queries, and the measurements a mechanism graph wants are usually supporting panels. This bound was not closed by opening candidate full texts."
}

{
  "instrument": "ENCODE Portal, type=Experiment, assay_title=TF ChIP-seq, status=released, per target label, counted from the @graph length with biosample term names collected",
  "counts": {
    "BRCA1": {
      "n": 7,
      "biosamples": [
        "GM12878",
        "H1",
        "HeLa-S3",
        "HepG2",
        "K562"
      ]
    },
    "CBX3": {
      "n": 4,
      "biosamples": [
        "GM12878",
        "HCT116",
        "K562"
      ]
    },
    "CBX1": {
      "n": 2,
      "biosamples": [
        "HepG2",
        "K562"
      ]
    },
    "CBX5": {
      "n": 4,
      "biosamples": [
        "GM12878",
        "H1",
        "HepG2",
        "K562"
      ]
    },
    "KDM5A": {
      "n": 3,
      "biosamples": [
        "A549",
        "H1",
        "HepG2"
      ]
    },
    "CTCF": {
      "n": 502,
      "biosamples": [
        "182 distinct biosamples including bone marrow, HL-60, K562, Loucy, DND-41 and primary B and T cells"
      ]
    },
    "TRIM28": {
      "n": 5,
      "biosamples": [
        "HEK293",
        "K562"
      ]
    },
    "SETDB1": {
      "n": 5,
      "biosamples": [
        "HEK293",
        "HepG2",
        "K562"
      ]
    },
    "BARD1": {
      "n": 0,
      "note": "CORRECTED 2026-09-22. Previously read 'HTTP 404 on the target.label facet - no ENCODE target record exists'. FALSE. /targets/BARD1-human/ returns HTTP 200 and the 404 was a property of the assay_title=TF+ChIP-seq filter, so it described the query and not the protein. BARD1 has an ENCODE target record and two released CRISPR RNA-seq experiments; what it lacks is a released TF ChIP-seq experiment, which is the narrower and true statement. RAD50 behaves identically (200 bare, 404 filtered); EXO1, DNA2, SUV39H1 and RBBP8 are genuine 404s on both endpoints."
    },
    "EXO1": {
      "n": 0,
      "note": "HTTP 404 - no target record"
    },
    "DNA2": {
      "n": 0,
      "note": "HTTP 404 - no target record"
    },
    "SUV39H1": {
      "n": 0,
      "note": "HTTP 404 - no target record; independently matches Q110's census"
    },
    "RBBP8": {
      "n": 0,
      "note": "HTTP 404 - no target record. CtIP, the short-range resection nuclease, has no ENCODE occupancy data either"
    }
  },
  "cross_check_against_Q110": "Q110 counted the same facet one day earlier and reported SETDB1 5, CBX5 4, CBX1 2, CBX3 4, EHMT2 3, TRIM28 5 and SUV39H1 0. Every overlapping figure matches. This is a reproducibility check on the same endpoint, not an independent confirmation.",
  "archives_NOT_swept": "GEO individual depositions, ChIP-Atlas, ReMap, PRIDE, and - most importantly for EXO1 and DNA2 - any resection-mapping archive (END-seq, BLESS, ssDNA-seq in the AsiSI/DIvA system). A DIvA resection dataset covering chr11q23 would answer part of this question with no wet work and was NOT queried. That is a named, unclosed, cheap check and it is recorded as such rather than left implicit."
}

{
  "from": "measured-not-analysed",
  "to": "never-measured",
  "why": "this entry classed BRCA1 and CBX3 as measured-not-analysed because ENCODE data existed and nobody had analysed it. Cycle 63 analysed it - 13 of 13 tracks, zero peaks, no signal above a class-matched null - so the public data is now spent. There is no remaining dataset that can advance this question for ANY of the six proteins, which is what never-measured means here.",
  "and_its_own_headline_sentence_is_now_false": "the entry called 'two of the six can be answered this week' its single most useful sentence. They were answered, and the answer was no, so the sentence no longer points anywhere. The 21 queries and the literature bound are unaffected and remain correct.",
  "what_this_costs": "the cheap route is gone. Advancing this question now requires wet work - ChIP in a damage state in a haematopoietic cell - which is the experiment absence-no-damage-state-occupancy-measurement-for-any-resection-factor-at-the-kmt2a-locus now carries.",
  "reported_by": "Q35; verified by the king against the beat's per-track table"
}