ARBA00026647 negative regulation of gene expression (GO:0010629)

id: ARBA00026647
description: Assigns GO:0010629 negative regulation of gene expression through 131 alternative condition
  sets of InterPro and CATH FunFam signatures, 59 of them with a taxon condition.
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00026647
  condition_sets:
  - number: 106
    conditions:
    - condition_type: FUNFAM
      value: 3.30.60.60:FF:000001
      curie: CATH.FUNFAM:3.30.60.60:FF:000001
      label: Histone acetyltransferase
      negated: false
    - condition_type: TAXON
      value: '4893'
      curie: NCBITaxon:4893
      label: Saccharomycetaceae
      negated: false
    notes: 'UniProtKB query, November 2026: 5 Swiss-Prot and 78 TrEMBL entries match. QuickGO, GO:0010629
      or a descendant on the Swiss-Prot entries: 2 with experimental evidence, 0 with other manual evidence
      only, 3 with IEA only, 0 with none. Examples: P34218 (SAS3_YEAST) GO:0030466 silent mating-type
      cassette heterochromatin formation, IMP, PMID:11731479; Q08649 (ESA1_YEAST) GO:0000183 rDNA heterochromatin
      formation, IGI, PMID:16436512.'
  go_annotations:
  - go_id: GO:0010629
    go_label: negative regulation of gene expression
    aspect: BP
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2021-10-20'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 131
review_summary: One of the 131 live condition sets was examined (set 106, a histone acetyltransferase
  FunFam in Saccharomycetaceae). Its Swiss-Prot matches include ESA1 and SAS3, both experimentally annotated
  to descendants of GO:0010629 (rDNA heterochromatin formation; silent mating-type cassette and subtelomeric
  heterochromatin formation). No wrongly annotated protein has been identified. The review is open.
action: UNDECIDED
action_rationale: The rule was not examined set by set. The one set checked is supported, and the single
  false positive alleged earlier is not one.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0010629
  label: negative regulation of gene expression
  assessment: UNDECIDED
  correct_examples:
  - Q08649
  - P34218
  notes: Q08649 (ESA1_YEAST) GO:0000183 rDNA heterochromatin formation, IMP and IGI, PMID:16436512 (SGD).
    P34218 (SAS3_YEAST) GO:0030466 silent mating-type cassette heterochromatin formation and GO:0031509
    subtelomeric heterochromatin formation, IMP, PMID:11731479 (SGD). These terms are descendants of GO:0010629
    (QuickGO). The other 130 sets were not examined.
corrections:
- date: '2026-11-10'
  withdrawn_claim: 'ESA1 (Q08649) is a documented false positive: a histone acetyltransferase that activates
    gene expression is wrongly annotated as a negative regulator.'
  correction: ESA1 has experimental annotation to rDNA heterochromatin formation, which is a kind of negative
    regulation of gene expression. A protein can both activate some genes and silence others.
  error_type: REFUTED_BY_CURATED_ANNOTATION
  evidence:
  - Q08649 GO:0000183 rDNA heterochromatin formation, IMP and IGI, PMID:16436512 (SGD)
  - 'QuickGO: ancestors of GO:0000183 include GO:0045814 negative regulation of gene expression, epigenetic,
    whose ancestors include GO:0010629'
  - 'Matching live set 106: 3.30.60.60:FF:000001 AND Saccharomycetaceae'
- date: '2026-11-10'
  withdrawn_claim: The rule applies eukaryotic silencing mechanisms across all domains of life because
    some condition sets lack a taxon condition.
  correction: A set without a taxon condition fires only where its signatures occur. No prokaryotic protein
    annotated by the rule was named.
  error_type: TAXON_MISREAD
  evidence:
  - 'Live rule: 131 sets, 59 with a taxon condition and 72 without (rest.uniprot.org/arba/ARBA00026647,
    2026-11-09)'
  - Old review cited no accession
- date: '2026-11-10'
  withdrawn_claim: GO:0010629 is too general because more specific child terms exist, so the rule should
    be deprecated.
  correction: A true general term is not grounds for removal.
  error_type: GENERAL_IS_NOT_WRONG
  evidence:
  - 'QuickGO: GO:0031047 and GO:0045814 are descendants of GO:0010629'
- date: '2026-11-10'
  withdrawn_claim: GO:0016458 (gene silencing) is an available more specific term.
  correction: GO:0016458 is obsolete.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - 'QuickGO: GO:0016458 "obsolete gene silencing", isObsolete true'
- date: '2026-11-10'
  withdrawn_claim: 131 condition sets far exceed the recommended maximum of 12; zinc finger and helicase
    domains are promiscuous.
  correction: The limit of 12 is the default of this repository's overlap-analysis tool. The review recorded
    no condition sets, so the statement about single domains was not based on the rule's conjunctions.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - 'src/ai_gene_review/etl/rule_analysis.py: max_condition_sets: int = 12 (default of the overlap-analysis
    tool)'
  - 'Old review: rule.condition_sets empty'