ARBA00027994 chromatin remodeling (GO:0006338)

id: ARBA00027994
description: >-
  ARBA rule assigning GO:0006338 chromatin remodeling through 167 alternative condition sets built
  from InterPro, CATH FunFam, PANTHER and taxon conditions.
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00027994
  condition_sets:
  - number: 1
    conditions:
    - condition_type: INTERPRO
      value: IPR001214
      curie: InterPro:IPR001214
      negated: false
    - condition_type: INTERPRO
      value: IPR003616
      curie: InterPro:IPR003616
      negated: false
    - condition_type: INTERPRO
      value: IPR011011
      curie: InterPro:IPR011011
      negated: false
    notes: >-
      SET domain with post-SET domain and a FYVE/PHD-type zinc finger: SET-domain histone methyltransferases.
      This is the only live set that uses IPR011011.
  - number: 7
    conditions:
    - condition_type: INTERPRO
      value: IPR001487
      curie: InterPro:IPR001487
      negated: false
    - condition_type: INTERPRO
      value: IPR036427
      curie: InterPro:IPR036427
      negated: false
    - condition_type: TAXON
      value: Taphrinomycotina
      label: Taphrinomycotina
      negated: false
    notes: Bromodomain signatures restricted to Taphrinomycotina.
  - number: 13
    conditions:
    - condition_type: INTERPRO
      value: IPR055197
      curie: InterPro:IPR055197
      negated: false
    notes: A single InterPro entry, specific to NSD-like histone-lysine N-methyltransferases.
  - number: 19
    conditions:
    - condition_type: INTERPRO
      value: IPR001005
      curie: InterPro:IPR001005
      negated: false
    - condition_type: INTERPRO
      value: IPR026489
      curie: InterPro:IPR026489
      negated: false
    - condition_type: INTERPRO
      value: IPR041343
      curie: InterPro:IPR041343
      negated: false
    notes: >-
      SANT/Myb domain with the CXC domain and the EZH1/EZH2 tri-helical domain: Polycomb EZH1/EZH2
      methyltransferases.
  go_annotations:
  - go_id: GO:0006338
    go_label: chromatin remodeling
    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: 167
review_summary: >-
  The live rule has 167 condition sets. Four (sets 1, 7, 13 and 19) were read for the identity of
  their signatures; each is a conjunction or a family-specific entry naming histone methyltransferases
  or bromodomain proteins. In GO, histone modifying activity (GO:0140993), histone deacetylase activity
  (GO:0004407) and ATP-dependent chromatin remodeler activity (GO:0140658) all sit under GO:0006338
  through part_of, so a rule that covers histone modifiers and ATP-dependent remodelers together follows
  the ontology. A reported false positive on human UBR7 (Q8N806) could not be reproduced: no live
  condition set matches its signatures and it carries no chromatin annotation in QuickGO. 163 sets
  were not examined, so no verdict is given.
action: UNDECIDED
action_rationale: >-
  Four of 167 condition sets were read and none was checked against annotated proteins. No current
  false positive is known.
suggested_modifications:
- Examine the condition sets against curated annotations of their Swiss-Prot members.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0006338
  label: chromatin remodeling
  assessment: UNDECIDED
  notes: >-
    QuickGO (2026-11-09, is_a and part_of ancestors): GO:0140993, GO:0004407 and GO:0140658 have GO:0006338
    as an ancestor; GO:0006335 DNA replication-dependent chromatin assembly does not. Q8N806 (UBR7)
    has InterPro IPR003126, IPR011011, IPR013083, IPR040204, IPR047506, IPR063242, IPR064051 and FunFam
    3.30.40.10:FF:000183; no live condition set is satisfied by these, and QuickGO returns no annotation
    of Q8N806 to GO:0006325 or its descendants.
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    GO:0006338 is misused because the rule groups ATP-dependent remodelers with histone-modifying
    enzymes.
  correction: >-
    GO itself places histone modifying activities and ATP-dependent chromatin remodeler activity under
    chromatin remodeling, so the grouping is the ontology's own.
  error_type: ONTOLOGY_MISREAD
  evidence:
  - 'QuickGO: GO:0140993 histone modifying activity has ancestor GO:0006338 (part_of)'
  - 'QuickGO: GO:0004407 histone deacetylase activity has ancestor GO:0006338'
  - 'QuickGO: GO:0140658 ATP-dependent chromatin remodeler activity has ancestor GO:0006338'
- date: '2026-11-10'
  withdrawn_claim: >-
    UBR7 (Q8N806) is falsely annotated by this rule because of the PHD-like zinc finger domain IPR011011.
  correction: >-
    The only live condition set containing IPR011011 also requires a SET domain and a post-SET domain,
    which UBR7 lacks; no live set matches UBR7 and it has no chromatin annotation now. The cited tracker
    item was not readable, so the original report is neither confirmed nor refuted for an earlier
    rule version.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - 'Live set 1: IPR001214 AND IPR003616 AND IPR011011'
  - UniProtKB Q8N806 InterPro cross-references do not include IPR001214 or IPR003616
  - 'QuickGO, 2026-11-09: no annotation of Q8N806 under GO:0006325'
- date: '2026-11-10'
  withdrawn_claim: >-
    Bromodomains (IPR001487) and SANT domains (IPR001005) are promiscuous, so the rule has a high
    false positive risk.
  correction: Both are used only inside conjunctions that narrow them to one family or clade.
  error_type: CONJUNCTION_IGNORED
  evidence:
  - 'Live set 7: IPR001487 AND IPR036427 AND Taphrinomycotina'
  - 'Live set 19: IPR001005 AND IPR026489 AND IPR041343 (EZH1/EZH2 tri-helical domain)'
- date: '2026-11-10'
  withdrawn_claim: Single-domain conditions such as IPR055197 lack specificity.
  correction: IPR055197 is a family-specific entry.
  error_type: WRONG_IDENTIFIER_MEANING
  evidence:
  - >-
    InterPro API: IPR055197 = Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger
- date: '2026-11-10'
  withdrawn_claim: 134 condition sets exceed any reasonable threshold, so the rule must be split.
  correction: Rule size is not evidence about correctness; the live rule has 167 sets.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - 'rest.uniprot.org/arba/ARBA00027994, 2026-11-09: 167 sets'
- date: '2026-11-10'
  withdrawn_claim: >-
    The rule should be split into rules asserting GO:0140658, GO:0140993 and GO:0004407 as more specific
    child terms.
  correction: >-
    These are molecular function terms, not children of the biological process term, and each implies
    GO:0006338 through part_of; no defect in the current consequent was shown.
  error_type: ONTOLOGY_MISREAD
  evidence:
  - 'QuickGO aspect of GO:0140658, GO:0140993, GO:0004407: molecular_function'