Q109 enumeration: the ten panel members that got no entry, the measurement that declined each, the papers read and not used, and four identifier traps measured on this panel

[
  "gene-phgdh",
  "gene-psat1",
  "gene-psph",
  "gene-shmt2",
  "gene-mthfd1",
  "gene-mthfd2",
  "gene-aldh1l2",
  "gene-cbs",
  "gene-cth",
  "gene-gpt2"
]

{
  "GLS": "RS4;11 d7 VTP -0.06 / EPZ +0.31 from a detected baseline of 6.84; MOLM13 -0.02; MV4;11 -0.54; all eight GPL570 probes within 0.49 in all three lines; DepMap mean -0.1803, 10.1% below -0.5; GLS[tiab] = 6,986 with a correctly formed fusion-scoped zero (non-empty translation, warninglist 'No items found.')",
  "SHMT1": "wrong direction - VTP +0.78, EPZ +1.05, baseline 3.02; all four array probes within 0.37 in all three lines; recorded inside gene-shmt2 as the paralogue observation where it is load-bearing",
  "MTHFD2L": "baseline 2.23 log2 CPM in RS4;11 and 1.05 in MOLM13, at or near the 1.0 floor; all seven array probes flat; UniProt Q9H903's mitochondrial assignment is ECO:0000250 BY SIMILARITY to a rat protein",
  "SLC1A5": "VTP -0.99, below the pre-declared 1.0 threshold by 0.01 - and its MV4;11 value is -1.61, so a different line would have included it. The arbitrariness is recorded rather than smoothed.",
  "SLC7A11": "VTP +0.13 / EPZ -1.84, margin +1.96, detected baseline 7.04 - the ONLY DOT1L-selective gene in 41. Declined by the |VTP| rule and flagged in the analysis entry as an anomaly, which is the weakest decline in this list.",
  "SLC3A2": "-1.26 with margin -0.33, on the compound-independent side; with SLC1A5 and SLC7A11 excluded the transport arm is n=2 and cannot be compared",
  "SLC7A5": "-1.34 with margin -0.19, same",
  "MTR_MTHFR_DHFR_TYMS": "declared as CONTEXT genes, not verdict genes; MTR +0.46, MTHFR -0.05, DHFR +0.29, TYMS baseline exactly 0.00. Their DepMap profiles are the finding and are recorded in gene-mthfd1: the one-carbon SINKS are pan-essential (MAT2A 95.2%, DHFR 69.8%, TYMS 51.2%) and the SOURCES are not.",
  "ASNS": "already has an entry. Re-measured: VTP -1.72, EPZ -1.47, margin -0.25, 86% reproduced - on the compound-INDEPENDENT side, which corrects how the standing asparaginase hypothesis should be read. Reported, not edited.",
  "ATF4_DDIT3_CHAC1_TRIB3_ATF5": "all have cycle-58 entries and served as the comparator arm; margins -0.085 to +0.095",
  "HOXA9": "excluded from the positive control - all 8 floor collisions in this run are HOXA9, with DMSO baselines of exactly 0.00 in RS4;11 day 2, MOLM13 day 2 and MOLM13 day 7, and -0.763 against a baseline of exactly 0.763 at RS4;11 day 7. Third dataset in this project in which HOXA9 has been unmeasurable."
}

{
  "33357456": "High Fructose Drives the Serine Synthesis Pathway in AML Cells (Cell Metab 2021) - directly relevant to this beat's unrecorded-medium caveat; unread",
  "35385727": "NADPH metabolism determines the leukemogenic capacity and drug resistance of AML cells (Cell Rep 2022) - the only fusion-scoped MTHFD1 record; unread",
  "36306790": "The m6A reader IGF2BP2 regulates glutamine metabolism in AML (Cancer Cell 2022) - one of two GPT2 leukaemia records; unread",
  "39579612": "Ailanthone targets the KMT2A-MEN1 complex in osteosarcoma (Phytomedicine 2025) - one of two menin-scoped PHGDH records; unread",
  "40328743": "m6A/IGF2BP3-driven serine biosynthesis fuels AML stemness and metabolic vulnerability (Nat Commun 2025) - may already contain the leukaemia PHGDH/PSAT1 dependency measurement gene-phgdh calls missing; unread",
  "40462988": "Serine auxotrophy is a targetable vulnerability driven by PSAT1 suppression in AML (bioRxiv 2025) - cited as counter-evidence in gene-psat1 while unread",
  "40752747": "The ALDH2-PKC-delta-SHMT2 axis and leukaemia stem cell self-renewal (Cancer Lett 2025); unread",
  "41151299": "Targeting serine metabolism vulnerability in omipalisib-resistant AML with PHGDH inhibitors (Biomed Pharmacother 2025); unread",
  "41759595": "Sodium aescinate induces renal cell ferroptosis through the ATF4/CTH/SQOR axis (Biochem Pharmacol 2026) - the only published ATF4-CTH link; unread",
  "42397900": "A targetable FTO/SLC7A11/CBS/CTH axis in NSCLC (Sci Adv 2026) - the only paper treating CBS, CTH and SLC7A11 as one axis; unread",
  "42304489_and_41764940": "ALDH1L2 in renal cell carcinoma organoids and small cell lung cancer - both make ALDH1L2 ferroptosis-suppressing and resistance-promoting, opposite to the pancreatic result cited in gene-aldh1l2; unread",
  "laboratories_publishing_here_and_not_cited": "the Rabinowitz and Vander Heiden one-carbon flux groups (no KMT2A work found) and the de Koning / Van Schaftingen serine-deficiency clinical group, whose disorder papers were verified bibliographically and used only through UniProt's curated summaries"
}

{
  "PHGDH_SERA": {
    "PHGDH[tiab]": 665,
    "fusion_scoped": 4,
    "SERA[tiab]": 135340,
    "SERA_fusion_scoped": 26,
    "id_set_intersection": 0,
    "verdict": "EXCLUDE, not union - a synonym with zero overlap names a different object; SERA is the UniProt entry-name stem and the plural of serum",
    "PGDH3[tiab]": 6,
    "3PGDH[tiab]": 34
  },
  "CBS": {
    "CBS[tiab]": 11871,
    "fusion_scoped_raw": 3,
    "fusion_scoped_genuine": 0,
    "false_positives": {
      "12686606": "CBs = Cajal bodies",
      "30727486": "Phytophthora root rot of Pinus pinea",
      "35180428": "CBSs = CTCF binding sites"
    },
    "registry_row_exists": false,
    "note": "two of the three contaminants are core vocabulary of THIS project's own subject area; reported for the coordinator to add a row"
  },
  "CTH_VSIG2": {
    "uniprot_gene_exact_reviewed_rows": 2,
    "P32929": "CGL_HUMAN, 405 aa, gene_primary CTH",
    "Q96IQ7": "VSIG2_HUMAN, 327 aa, gene_primary VSIG2, synonyms CTH and CTXL",
    "ensembl_first_hit": "ENSG00000019102 = VSIG2; correct ENSG00000116761",
    "rule_62_instance": 3,
    "previous_instances": [
      "DDIT3",
      "SFN"
    ],
    "registry_row_exists": true,
    "registry_row_describes": "the ENSEMBL failure only",
    "refinement_proposed": "a collision row should name the OBJECT PAIR and both accessions, not the instrument that happened to fail"
  },
  "PSAT1_PSA": {
    "PSAT1[tiab]": 352,
    "PSA[tiab]": 51994,
    "PSAT[tiab]": 327,
    "EPIP[tiab]": 62,
    "verdict": "EXCLUDE PSA (prostate-specific antigen), but on the token's known referent and NOT on a measured id-set intersection - the weak form, flagged in gene-psat1"
  }
}

{
  "rule_88_registry_grep_command_returns_empty_for_every_symbol": "docs/QUEEN_BRIEF.md rule 88 prints `[r for r in d if 'BACH1' in json.dumps(r)]` over data/symbol-collisions.json. The file is a DICT with keys _comment, generated, verified_against, collisions, non_gene_antigens, so iterating it yields five key strings and the comprehension returns [] for every symbol. Verified this session: the documented command returns [] for BACH1 while d['collisions'] returns 1 match. The 169 rows live under d['collisions']. The rule written to stop beats rediscovering collisions ships a command whose failure mode is a FALSE CLEAR.",
  "correct_form": "python -c \"import io,json;d=json.load(io.open('data/symbol-collisions.json',encoding='utf-8'));print([r for r in d['collisions'] if 'BACH1' in json.dumps(r)])\"",
  "panel_maximum_depmap_guard_is_blind_to_a_single_empty_payload": "The brief requires a payload guard keyed to the panel MAXIMUM clearing ~1,000 screens rather than a per-row floor, which is right for detecting truncation and was PASS here at 1,258. But POLR2A - the canonical pan-essential control - returned 0 tissue blocks and 0 screens with its approvedSymbol readback PASSING. A panel-maximum guard cannot see a single gene's empty payload. The script prints per-gene n_tissue_blocks and n_screens so it was visible, but it did not fail. A companion per-gene zero-screen check is needed."
}

{
  "ana-the-serine-arm-replicates-in-a-third-aff1-line-from-another-lab-but-the-stress-output-genes-do-not": "its data.did_not_replicate_the_isr_output lists CTH as '+0.24 against -1.57 in RS4;11'. CTH's MV4;11 Safe3 DMSO baseline is 0.29 log2 CPM, BELOW a 1.0 log2 CPM floor - an absence of signal, not a non-replication. CTH could not be tested in MV4;11. The source that settles it is that entry's own results.json, read from disk 2026-09-22. Also worth noting in the same block: DDIT3 (1.93), CHAC1 (1.90) and TRIB3 (3.00) are all near the floor in MV4;11, so the 'ISR did not replicate' conclusion is partly a detection question too.",
  "hyp-menin-inhibition-collapses-the-serine-asns-programme-and-should-resensitise-kmt2a-r-all-to-asparaginase": "ASNS's compound margin is -0.25 with 86% of the effect reproduced by EPZ5676, so ASNS is on the compound-INDEPENDENT side of the split this beat measures. The asparaginase prediction therefore does not inherit any menin-selectivity, and the entry should say so. No citation beyond this beat's own results.json is needed because the entry's own numbers are consistent with it - what is missing there is the EPZ5676 column.",
  "ana-does-atf4s-own-transcript-move-under-a-menin-inhibitor": "its data block lists PHGDH '-3.24 / -1.52' inside the_discriminating_arm alongside MEIS1, MEF2C and PBX3. That row is correct and is, in retrospect, the single most consequential number in that entry - it is the observation this whole beat is built on, and it appears there as an unremarked fourth item in a list of menin targets. Suggested change: promote it to prose, because a reader of that entry cannot currently tell that a serine-pathway gene is sitting in the menin-discriminating arm."
}