PPIL4 - a spliceosomal cyclophilin whose BioID neighbourhood is the widest overlap with this graph's subject matter of any bait

[
  "AFF4",
  "ELL",
  "MLLT1",
  "CDK9",
  "CCNT1",
  "KMT2A",
  "PSIP1",
  "WDR5",
  "KAT7",
  "ICE1",
  "ICE2",
  "PAF1",
  "BRD4",
  "NELFE",
  "ASH2L",
  "ELOA",
  "CDC73",
  "RTF1",
  "KMT2D",
  "SETD1A",
  "SETD1B",
  "HCFC1",
  "SIRT1",
  "HDAC1",
  "HDAC2",
  "CHD8",
  "ARID1A",
  "RUNX1",
  "IGF2BP2",
  "HNRNPA2B1",
  "YTHDC1",
  "RBM15"
]

{
  "chronos_mean_kmt2a_rearranged": -0.8597,
  "chronos_mean_other_leukaemia": -0.9369,
  "difference": 0.0772,
  "pan_essentiality_all_lines": -0.9391,
  "selectivity_rank": 16264,
  "rank_denominator": 17728,
  "provenance": "Joined 2026-09-21 from analyses/depmap-kmt2a-selective-scan-full (generated 2026-09-19T10:12:06Z), the project's own genome-wide scan over 11 KMT2A-rearranged and 43 other leukaemia DepMap lines. NOT re-fetched and NOT independent of that scan: every caveat it carries applies here, including that the KMT2A-rearranged arm is a small number of lines drawn from nine individuals, that the rank denominator is 17,728 genes, and that a difference is not a dependency. Added because only 26 of 308 gene entries carried this number, which made any KMT2A-selectivity question answerable for 8% of the corpus.",
  "how_to_read": "A negative difference means MORE required in KMT2A-rearranged lines than in other leukaemia lines. A rank near 17,728 is ANTI-selective. Neither is evidence of a fusion-driven dependency on its own: check pan_essentiality_all_lines before calling anything selective, and note that a paralogue-redundant gene can score near zero for reasons that have nothing to do with this disease - see ana-the-paralogue-redundancy-excuse-is-not-tested-and-my-proxy-decided-the-answer."
}

{
  "CONSTITUTIVE": "NUCLEUS, PREDICTED - AND THIS PROTEIN HAS NEVER BEEN IMAGED. UniProt Q8WUA2 (fetched live 2026-09-21) carries ONE subcellular location value, 'Nucleus', on a bare ECO:0000305 - CURATOR INFERENCE, with no experimental attribution of any kind, no location note and no annotated NLS in the retrieved feature table [E_q91_ppil4_loc1]. This is the weakest evidence tier in the whole tranche: not an over-reaching ECO:0000269 (SMARCD1), not a transfer from an orthologue (SGF29, SMC3), not an empty evidence list on a well-studied protein (SMARCB1, SIAH1), but an explicit curator inference on a protein with a nine-record literature.",
  "WHERE_THE_INFERENCE_CAME_FROM": "Almost certainly from the sole primary source. The cloning paper reports that besides the PPIase motif, PPIL4 has an RNA RECOGNITION MOTIF (RRM), A PAIR OF BIPARTITE NUCLEAR TARGETING SEQUENCES, and a lysine-rich domain - and it calls PPIL4 a 'novel NUCLEAR RNA-binding cyclophilin-like gene' IN ITS TITLE on that basis. The nuclear claim is a SEQUENCE PREDICTION from bipartite NLS motifs in a cDNA isolated from a human fetal brain library, not a measurement [E_q91_ppil4_loc2]."
}

{
  "measured_in": "NOTHING. The cDNA came from a human FETAL BRAIN library and the expression evidence is RT-PCR across tissues [E_q91_ppil4_loc2]; the structural work is in vitro on purified spliceosomes [E_q91_ppil4_loc3]. There is no cell-biological experiment on PPIL4 anywhere.",
  "the_only_cell_type_connection_this_entry_has": "K562, and it is as a BAIT rather than as a subject: PPIL4 is one of fifty RNA-binding proteins used as a BioID2 bait in K562, and its 671-prey neighbourhood reaches thirty-two proteins this graph holds entries for, including AFF4, ELL, MLLT1, CDK9, CCNT1, KMT2A, PSIP1 and WDR5 - while reaching NEITHER AFF1 NOR MEN1 (this entry's E1). Proximity labelling in a leukaemia line is the only experiment that has ever put this protein in a named cell.",
  "never": "No localisation in any cell type, let alone a KMT2A-rearranged one."
}

{
  "none_recorded": "No cell-cycle, stress, damage or differentiation behaviour of PPIL4 is reported anywhere retrieved. For a protein with nine records this is unsurprising and it should be recorded as an absence of effort rather than an absence of phenomena.",
  "the_state_it_implies": "PPIL4 is the PPIase that rides with the spliceosome through catalytic activation, a stage driven by the helicases PRP2/DHX16 and Aquarius [E_q91_ppil4_loc3]. Its 'state' is a step in the splicing cycle rather than a cellular state - which is a reason its distribution might be uninformative even if measured, and a reason to measure it once rather than repeatedly."
}

{
  "date": "2026-09-22",
  "tool": "NCBI esearch db=pubmed",
  "run_by": "Q91",
  "queries": [
    {
      "query": "PPIL4[tiab]",
      "querytranslation": "\"PPIL4\"[Title/Abstract]",
      "count": 9,
      "role": "operand control - AND the total literature. Nine records."
    },
    {
      "query": "PPIL4[tiab] AND (nuclear[tiab] OR speckle[tiab] OR spliceosome[tiab] OR localization[tiab])",
      "querytranslation": "\"PPIL4\"[Title/Abstract] AND (\"nuclear\"[Title/Abstract] OR \"speckle\"[Title/Abstract] OR \"spliceosome\"[Title/Abstract] OR \"localization\"[Title/Abstract])",
      "count": 2,
      "both_read": true,
      "containing_an_image_of_the_protein_in_a_cell": 0
    },
    {
      "query": "PPIL4[tiab] AND MLL[tiab]",
      "querytranslation": "\"PPIL4\"[Title/Abstract] AND \"MLL\"[Title/Abstract]",
      "count": 0
    },
    {
      "query": "PPIL4[tiab] AND KMT2A[tiab]",
      "querytranslation": "\"PPIL4\"[Title/Abstract] AND \"KMT2A\"[Title/Abstract]",
      "count": 0
    }
  ],
  "reading": "With a nine-record total literature, a title-and-abstract bound is very nearly a bound on the papers themselves - the usual rule-80 escape hatch (the measurement is in a supporting figure) has only nine papers to hide in, and two of them were read. This is the most defensible bounded absence in the tranche. The aliases CypL4 and HDCME13P were not run as separate operands.",
  "absence_class": "never-measured"
}