title: 'Re-review of REMOVE actions in human gene reviews: row-level changes' date: '2026-11-10' issue: https://github.com/ai4curation/ai-gene-review/issues/4097 base_commit: f0a0e4c53 scope: remove_rows_at_start: 23802 bare_protein_binding_rows: 22013 substantive_rows: 1789 rows_reactioned: 408 remove_rows_kept_with_revised_reason: 9 source_defects_recorded: 64 reviews_edited: 222 remove_rows_at_end: 23394 description: 'changes lists every row whose review block was edited: rows that moved from REMOVE to another action, and rows that stay REMOVE with a corrected reason or a recorded source defect. retained_with_note lists REMOVE rows that were examined closely and left in place; close_call marks judgement calls that a curator might decide differently. index is the position of the row in existing_annotations at base_commit; term, evidence_type and reference identify the row if the file is re-fetched. A note that names further indexes covers those rows as well. consistency_followups lists rows that were not REMOVE but were changed so that all rows of a re-adjudicated term agree; they are not counted in scope.' rules: same-term-kept: The same term is kept on another row of the review. Rows that share a term are judged alike, so the row takes the action of its sibling; a defect in the row's own reference or evidence is recorded as a source defect. ancestor-of-kept: The removed term is an ancestor of a term kept in the review, so it is true; it is recorded as TOO_GENERAL. true-but-broad: The reason conceded that the term is true but broad; it is kept or refined, not removed. reason-concedes-truth: The reason for removal conceded that the claim is true (uninformative, redundant, better described elsewhere). A true claim is kept, as core or non-core. general-to-specific: A correct but general term is refined to the specific term the evidence supports (MODIFY). lateral-correction: The observation is real but the term misstates it (wrong sign, wrong cofactor, wrong compartment); it is redirected to the term the evidence supports (MODIFY). claim-established: An electronic or similarity transfer whose donor annotation comes from a targeted experiment that establishes the claim; kept as non-core. electronic-unsupported-plausible: An electronic or similarity transfer whose donor annotation is experimental but over-reads a phenotype or downstream consequence; marked as an over-annotation instead of removed. downstream-readout: The term describes a downstream readout of the established function; marked as an over-annotation. experimental-incomplete-evidence: An experimental or curated row removed on the strength of an abstract or without access to the source; left UNDECIDED, or kept where the function is clearly correct. experimental-fulltext-supports: The full text of the cited paper supports the annotation. curated-statement: A curated author statement (TAS, NAS, IC) whose claim is plausible and uncontradicted; kept or marked instead of removed. omics-location: A location from proteomics, high-throughput imaging or the Human Protein Atlas with no positive contradiction; marked as an over-annotation, or kept as non-core where independent evidence agrees. omics-function: A molecular function inferred from an omics hit (cadherin interactome, RNA interactome capture); marked as an over-annotation. expression-only: A process annotated from an expression change of the gene (IEP, HEP and expression-based direct assays); marked as an over-annotation. reactome-location: A location taken from a Reactome reaction that is plausible for the reaction but not a place of residence; kept as non-core or marked. er-transit: An endoplasmic reticulum row on a secreted or membrane protein that rests on transit; marked as an over-annotation, following the organelle policy. organelle-root: 'A root organelle term handled under the organelle policy: the organelle claim holds, so the row is kept.' cross-gene-consistency: Twin genes or subunits of one complex are treated alike across reviews. iba-node-not-examined: A phylogenetic annotation removed without an argument against the node placement. promiscuous-activity: A measured secondary enzyme activity handled under the promiscuous-activity tiers. remove-rereasoned: REMOVE stands; the reason was corrected or a source defect was recorded. source-defect-recorded: REMOVE stands and the action is unchanged; the error in the source record that justifies it is recorded as a structured source defect. protein-binding-audit: Bare protein binding row (sanctioned REMOVE); a source defect found during the policy audit was recorded. changes: - gene: AADAC index: 35 term: id: GO:0017171 label: serine hydrolase activity evidence_type: IDA reference: PMID:17936933 old_action: REMOVE new_action: ACCEPT rule: same-term-kept source_defects: - WRONG_EVIDENCE_CODE - gene: ABCE1 index: 35 term: id: GO:0016020 label: membrane evidence_type: HDA reference: PMID:19946888 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: ABCF2 index: 5 term: id: GO:0016020 label: membrane evidence_type: HDA reference: PMID:19946888 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: ACSL1 index: 30 term: id: GO:0009410 label: response to xenobiotic stimulus evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: ACTR1B index: 11 term: id: GO:0005576 label: extracellular region evidence_type: TAS reference: Reactome:R-HSA-6798748 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: ACTR1B index: 12 term: id: GO:0005576 label: extracellular region evidence_type: TAS reference: Reactome:R-HSA-6800434 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: ADGRA2 index: 56 term: id: GO:0004930 label: G protein-coupled receptor activity evidence_type: TAS reference: PMID:15203201 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept source_defects: - WRONG_EVIDENCE_CODE - gene: ADGRA2 index: 57 term: id: GO:0007186 label: G protein-coupled receptor signaling pathway evidence_type: TAS reference: PMID:15203201 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept source_defects: - WRONG_EVIDENCE_CODE - gene: ADIPOQ index: 96 term: id: GO:0120162 label: positive regulation of cold-induced thermogenesis evidence_type: ISS reference: PMID:24531262 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: same-term-kept source_defects: - WRONG_REFERENCE - gene: ADIPOQ index: 99 term: id: GO:0120163 label: negative regulation of cold-induced thermogenesis evidence_type: ISS reference: PMID:26166748 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: same-term-kept source_defects: - WRONG_REFERENCE - gene: AHSA1 index: 23 term: id: GO:0045296 label: cadherin binding evidence_type: HDA reference: PMID:25468996 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-function - gene: AMPD3 index: 15 term: id: GO:0046039 label: GTP metabolic process evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: ANLN index: 20 term: id: GO:0045296 label: cadherin binding evidence_type: HDA reference: PMID:25468996 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-function - gene: APAF1 index: 18 term: id: GO:0005576 label: extracellular region evidence_type: TAS reference: Reactome:R-HSA-6798748 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: APAF1 index: 19 term: id: GO:0005576 label: extracellular region evidence_type: TAS reference: Reactome:R-HSA-6800434 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: ARF1 index: 21 term: id: GO:0030017 label: sarcomere evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: ARL8A index: 24 term: id: GO:0005886 label: plasma membrane evidence_type: TAS reference: Reactome:R-HSA-6798739 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: curated-statement - gene: ARL8A index: 25 term: id: GO:0005886 label: plasma membrane evidence_type: TAS reference: Reactome:R-HSA-6800426 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: curated-statement - gene: ARL8A index: 26 term: id: GO:0035577 label: azurophil granule membrane evidence_type: TAS reference: Reactome:R-HSA-6798739 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: curated-statement - gene: ARL8A index: 27 term: id: GO:0101003 label: ficolin-1-rich granule membrane evidence_type: TAS reference: Reactome:R-HSA-6800426 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: curated-statement - gene: ARNT index: 8 term: id: GO:0005737 label: cytoplasm evidence_type: IEA reference: GO_REF:0000120 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: ARPP19 index: 6 term: id: GO:0005102 label: signaling receptor binding evidence_type: IDA reference: PMID:9653196 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: ARPP19 index: 14 term: id: GO:0015459 label: potassium channel regulator activity evidence_type: IDA reference: PMID:9653196 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: ARPP19 index: 17 term: id: GO:0045722 label: positive regulation of gluconeogenesis evidence_type: IDA reference: PMID:9653196 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: ARPP19 index: 18 term: id: GO:0046326 label: positive regulation of D-glucose import across plasma membrane evidence_type: NAS reference: PMID:9653196 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: ASCC3 index: 48 term: id: GO:0016020 label: membrane evidence_type: HDA reference: PMID:19946888 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: ASCL1 index: 29 term: id: GO:0045665 label: negative regulation of neuron differentiation evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: ASCL1 index: 62 term: id: GO:0045665 label: negative regulation of neuron differentiation evidence_type: IDA reference: PMID:12000752 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: ATF3 index: 56 term: id: GO:0000122 label: negative regulation of transcription by RNA polymerase II evidence_type: TAS reference: PMID:14685163 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: ATF3 index: 64 term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific evidence_type: IDA reference: PMID:16300731 old_action: REMOVE new_action: ACCEPT rule: same-term-kept source_defects: - WRONG_GENE_PRODUCT - gene: ATF3 index: 75 term: id: GO:0045944 label: positive regulation of transcription by RNA polymerase II evidence_type: IDA reference: PMID:16300731 old_action: REMOVE new_action: ACCEPT rule: same-term-kept source_defects: - WRONG_GENE_PRODUCT - gene: ATP23 index: 6 term: id: GO:0005886 label: plasma membrane evidence_type: IDA reference: GO_REF:0000052 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: ATP23 index: 7 term: id: GO:0030054 label: cell junction evidence_type: IDA reference: GO_REF:0000052 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: ATP23 index: 10 term: id: GO:0005958 label: DNA-dependent protein kinase-DNA ligase 4 complex evidence_type: NAS reference: PMID:10219089 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: curated-statement - gene: ATP23 index: 11 term: id: GO:0006303 label: double-strand break repair via nonhomologous end joining evidence_type: TAS reference: PMID:10219089 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: curated-statement - gene: ATP5IF1 index: 25 term: id: GO:0032991 label: protein-containing complex evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: true-but-broad - gene: ATPAF2 index: 21 term: id: GO:0016607 label: nuclear speck evidence_type: IDA reference: GO_REF:0000054 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: AZGP1 index: 0 term: id: GO:0001580 label: detection of chemical stimulus involved in sensory perception of bitter taste evidence_type: IDA reference: PMID:24248522 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: experimental-incomplete-evidence - gene: B2M index: 96 term: id: GO:0005925 label: focal adhesion evidence_type: HDA reference: PMID:21423176 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: BAG2 index: 60 term: id: GO:0019538 label: protein metabolic process evidence_type: IDA reference: PMID:9873015 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: BAG6 index: 1 term: id: GO:0031593 label: polyubiquitin modification-dependent protein binding evidence_type: IBA reference: GO_REF:0000033 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: BAG6 index: 10 term: id: GO:0030544 label: Hsp70 protein binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: BAG6 index: 11 term: id: GO:0031593 label: polyubiquitin modification-dependent protein binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: BAG6 index: 19 term: id: GO:0070628 label: proteasome binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: BAG6 index: 48 term: id: GO:0140677 label: molecular function activator activity evidence_type: IEP reference: PMID:25713138 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: BAG6 index: 94 term: id: GO:0031593 label: polyubiquitin modification-dependent protein binding evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: BAG6 index: 101 term: id: GO:0070628 label: proteasome binding evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: BAK1 index: 83 term: id: GO:0005829 label: cytosol evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: BAK1 index: 86 term: id: GO:0008285 label: negative regulation of cell population proliferation evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: BAK1 index: 97 term: id: GO:0031334 label: positive regulation of protein-containing complex assembly evidence_type: IDA reference: PMID:9111042 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: experimental-incomplete-evidence - gene: BAK1 index: 122 term: id: GO:0044877 label: protein-containing complex binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: BAK1 index: 124 term: id: GO:0045862 label: positive regulation of proteolysis evidence_type: IDA reference: PMID:18387192 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: BAK1 index: 129 term: id: GO:0051049 label: regulation of transport evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: BAK1 index: 131 term: id: GO:0051246 label: regulation of protein metabolic process evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: BAK1 index: 152 term: id: GO:1902531 label: regulation of intracellular signal transduction evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: BAX index: 143 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-3700984 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: BAX index: 145 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-9008839 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: BAX index: 165 term: id: GO:0031334 label: positive regulation of protein-containing complex assembly evidence_type: IDA reference: PMID:9111042 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: same-term-kept - gene: BAX index: 170 term: id: GO:0033554 label: cellular response to stress evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: BAX index: 209 term: id: GO:0070062 label: extracellular exosome evidence_type: HDA reference: PMID:20458337 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: BAX index: 229 term: id: GO:0097435 label: supramolecular fiber organization evidence_type: IDA reference: PMID:31690630 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: experimental-fulltext-supports - gene: BAX index: 232 term: id: GO:1902531 label: regulation of intracellular signal transduction evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: BBC3 index: 35 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-139913 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: same-term-kept - gene: BBC3 index: 37 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-140221 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: same-term-kept - gene: BBC3 index: 38 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-9622667 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: same-term-kept - gene: BBC3 index: 61 term: id: GO:1903896 label: positive regulation of IRE1-mediated unfolded protein response evidence_type: TAS reference: PMID:22013210 old_action: REMOVE new_action: UNDECIDED rule: curated-statement - gene: BCL2 index: 146 term: id: GO:0043565 label: sequence-specific DNA binding evidence_type: IDA reference: PMID:12086670 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: BCL2L11 index: 82 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-8952232 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: BCL2L11 index: 83 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-9699574 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: BCL2L11 index: 86 term: id: GO:0008017 label: microtubule binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: BCL2L11 index: 108 term: id: GO:1903896 label: positive regulation of IRE1-mediated unfolded protein response evidence_type: TAS reference: PMID:22013210 old_action: REMOVE new_action: UNDECIDED rule: curated-statement - gene: BID index: 66 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-6791291 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: CALCA index: 8 term: id: GO:0005515 label: protein binding evidence_type: IPI reference: PMID:17689535 old_action: REMOVE new_action: REMOVE rule: protein-binding-audit source_defects: - WRONG_GENE_PRODUCT - gene: CALCA index: 32 term: id: GO:0002548 label: monocyte chemotaxis evidence_type: IDA reference: PMID:15248232 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: CASP14 index: 12 term: id: GO:0045095 label: keratin filament evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: CDC25C index: 46 term: id: GO:0005758 label: mitochondrial intermembrane space evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: CFLAR index: 6 term: id: GO:0005123 label: death receptor binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: CFLAR index: 69 term: id: GO:0044877 label: protein-containing complex binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: CGA index: 46 term: id: GO:0035773 label: insulin secretion involved in cellular response to glucose stimulus evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: CHEK1 index: 46 term: id: GO:0005576 label: extracellular region evidence_type: HDA reference: PMID:23580065 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: CHEK1 index: 88 term: id: GO:0032991 label: protein-containing complex evidence_type: IDA reference: PMID:26296656 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: true-but-broad - gene: CHMP1B index: 12 term: id: GO:0007034 label: vacuolar transport evidence_type: IEA reference: GO_REF:0000002 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: CHMP1B index: 86 term: id: GO:0070062 label: extracellular exosome evidence_type: HDA reference: PMID:23533145 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: omics-location - gene: CHMP1B index: 90 term: id: GO:0070062 label: extracellular exosome evidence_type: HDA reference: PMID:19056867 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: omics-location - gene: CHMP1B index: 91 term: id: GO:0070062 label: extracellular exosome evidence_type: HDA reference: PMID:20458337 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: omics-location - gene: CKAP2 index: 18 term: id: GO:0045944 label: positive regulation of transcription by RNA polymerase II evidence_type: IGI reference: PMID:16061649 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: experimental-incomplete-evidence - gene: COP1 index: 11 term: id: GO:0000139 label: Golgi membrane evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: CRY1 index: 11 term: id: GO:0019902 label: phosphatase binding evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: CRY1 index: 18 term: id: GO:0005739 label: mitochondrion evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: organelle-root - gene: CRY1 index: 22 term: id: GO:0014823 label: response to activity evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: CRY1 index: 26 term: id: GO:0019915 label: lipid storage evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: CRY1 index: 27 term: id: GO:0031397 label: negative regulation of protein ubiquitination evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: CRY1 index: 28 term: id: GO:0031398 label: positive regulation of protein ubiquitination evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: CRY1 index: 35 term: id: GO:0042770 label: signal transduction in response to DNA damage evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: CRY1 index: 44 term: id: GO:2000001 label: regulation of DNA damage checkpoint evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: CRY1 index: 50 term: id: GO:0014823 label: response to activity evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: CRY1 index: 54 term: id: GO:0031398 label: positive regulation of protein ubiquitination evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: CRY1 index: 59 term: id: GO:0031397 label: negative regulation of protein ubiquitination evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: CRY1 index: 65 term: id: GO:0042770 label: signal transduction in response to DNA damage evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: CRY1 index: 66 term: id: GO:2000001 label: regulation of DNA damage checkpoint evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: CRY1 index: 76 term: id: GO:0019902 label: phosphatase binding evidence_type: IPI reference: PMID:9383998 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: CRY2 index: 18 term: id: GO:0005739 label: mitochondrion evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: organelle-root - gene: CRY2 index: 57 term: id: GO:0005576 label: extracellular region evidence_type: IDA reference: PMID:9753616 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: CRY2 index: 58 term: id: GO:2000118 label: regulation of sodium-dependent phosphate transport evidence_type: IDA reference: PMID:9753616 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: CTC1 index: 43 term: id: GO:1990879 label: CST complex evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: ACCEPT rule: same-term-kept source_defects: - WRONG_WITH_FROM - gene: CTNS index: 52 term: id: GO:0050890 label: cognition evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: CYC1 index: 22 term: id: GO:0005634 label: nucleus evidence_type: HDA reference: PMID:21630459 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: DCN index: 45 term: id: GO:0003723 label: RNA binding evidence_type: HDA reference: PMID:22658674 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-function - gene: DDB1 index: 3 term: id: GO:0003676 label: nucleic acid binding evidence_type: IEA reference: GO_REF:0000002 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: DPEP1 index: 50 term: id: GO:0050667 label: homocysteine metabolic process evidence_type: IDA reference: PMID:20031578 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: experimental-fulltext-supports - gene: DPEP1 index: 52 term: id: GO:0072341 label: modified amino acid binding evidence_type: IDA reference: PMID:20031578 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: experimental-fulltext-supports - gene: EFEMP1 index: 71 term: id: GO:0043010 label: camera-type eye development evidence_type: IEP reference: PMID:25406291 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: EFEMP1 index: 72 term: id: GO:0048048 label: embryonic eye morphogenesis evidence_type: IEP reference: PMID:25406291 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: EFEMP1 index: 73 term: id: GO:0048050 label: post-embryonic eye morphogenesis evidence_type: IEP reference: PMID:25406291 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: ELAVL1 index: 18 term: id: GO:0005783 label: endoplasmic reticulum evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: organelle-root - gene: EN1 index: 28 term: id: GO:0009653 label: anatomical structure morphogenesis evidence_type: TAS reference: PMID:8094370 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: ERN1 index: 52 term: id: GO:0019899 label: enzyme binding evidence_type: IPI reference: PMID:23103912 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: FADD index: 154 term: id: GO:0033612 label: receptor serine/threonine kinase binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: REMOVE rule: remove-rereasoned reason_revised: true - gene: FADD index: 162 term: id: GO:0042802 label: identical protein binding evidence_type: IPI reference: PMID:25502805 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: FADD index: 163 term: id: GO:0042802 label: identical protein binding evidence_type: IPI reference: PMID:30561431 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: FADD index: 164 term: id: GO:0042802 label: identical protein binding evidence_type: IPI reference: PMID:31515488 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: FADD index: 165 term: id: GO:0042802 label: identical protein binding evidence_type: IPI reference: PMID:32296183 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: FCER1G index: 51 term: id: GO:0019863 label: IgE binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: reason-concedes-truth - gene: FEN1 index: 57 term: id: GO:0016020 label: membrane evidence_type: HDA reference: PMID:19946888 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: FGF7 index: 63 term: id: GO:0010463 label: mesenchymal cell proliferation evidence_type: IDA reference: PMID:11023837 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_REFERENCE - gene: FN3K index: 18 term: id: GO:0030855 label: epithelial cell differentiation evidence_type: IEP reference: PMID:21492153 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: expression-only - gene: FNTA index: 9 term: id: GO:0005886 label: plasma membrane evidence_type: IEA reference: GO_REF:0000108 old_action: REMOVE new_action: REMOVE rule: remove-rereasoned reason_revised: true - gene: FZD7 index: 10 term: id: GO:0005109 label: frizzled binding evidence_type: IPI reference: PMID:19188438 old_action: REMOVE new_action: REMOVE rule: remove-rereasoned source_defects: - WRONG_TERM reason_revised: true - gene: FZD7 index: 15 term: id: GO:0016055 label: Wnt signaling pathway evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: FZD7 index: 16 term: id: GO:0007165 label: signal transduction evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: FZD7 index: 17 term: id: GO:0007166 label: cell surface receptor signaling pathway evidence_type: IEA reference: GO_REF:0000002 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: FZD7 index: 18 term: id: GO:0007186 label: G protein-coupled receptor signaling pathway evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: ancestor-of-kept - gene: FZD7 index: 19 term: id: GO:0060828 label: regulation of canonical Wnt signaling pathway evidence_type: IMP reference: PMID:9707618 old_action: REMOVE new_action: MODIFY rule: lateral-correction replacement_terms: - GO:0060070 canonical Wnt signaling pathway - gene: FZD7 index: 24 term: id: GO:0006355 label: regulation of DNA-templated transcription evidence_type: IMP reference: PMID:18681827 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: downstream-readout - gene: FZD7 index: 25 term: id: GO:0045893 label: positive regulation of DNA-templated transcription evidence_type: IDA reference: PMID:18215320 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: downstream-readout - gene: FZD7 index: 30 term: id: GO:0042327 label: positive regulation of phosphorylation evidence_type: IDA reference: PMID:18256285 old_action: REMOVE new_action: MODIFY rule: general-to-specific replacement_terms: - GO:0046330 positive regulation of JNK cascade - gene: FZD7 index: 51 term: id: GO:0045893 label: positive regulation of DNA-templated transcription evidence_type: IMP reference: PMID:19773752 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: downstream-readout - gene: GAPDH index: 19 term: id: GO:0050661 label: NADP binding evidence_type: IEA reference: GO_REF:0000002 old_action: REMOVE new_action: REMOVE rule: remove-rereasoned reason_revised: true - gene: GAPDH index: 63 term: id: GO:0097718 label: disordered domain specific binding evidence_type: IPI reference: PMID:11785981 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: GAPDH index: 64 term: id: GO:0016241 label: regulation of macroautophagy evidence_type: TAS reference: PMID:26626483 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: GAPDH index: 79 term: id: GO:0017148 label: negative regulation of translation evidence_type: IMP reference: PMID:15479637 old_action: REMOVE new_action: ACCEPT rule: claim-established - gene: GAPDH index: 80 term: id: GO:0017148 label: negative regulation of translation evidence_type: IDA reference: PMID:23071094 old_action: REMOVE new_action: ACCEPT rule: claim-established - gene: GAPDH index: 81 term: id: GO:0071346 label: cellular response to type II interferon evidence_type: IDA reference: PMID:15479637 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: GAPDH index: 82 term: id: GO:1990904 label: ribonucleoprotein complex evidence_type: IDA reference: PMID:15479637 old_action: REMOVE new_action: MODIFY rule: general-to-specific replacement_terms: - GO:0097452 GAIT complex - gene: GAPDH index: 85 term: id: GO:0015630 label: microtubule cytoskeleton evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: GAPDH index: 86 term: id: GO:0000226 label: microtubule cytoskeleton organization evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: GAPDH index: 87 term: id: GO:0008017 label: microtubule binding evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: GAPDH index: 88 term: id: GO:0005811 label: lipid droplet evidence_type: IDA reference: PMID:14741744 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: GAPDH index: 92 term: id: GO:0035606 label: peptidyl-cysteine S-trans-nitrosylation evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: GAPDH index: 93 term: id: GO:0050821 label: protein stabilization evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: GAPDH index: 94 term: id: GO:0051402 label: neuron apoptotic process evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: GATA4 index: 68 term: id: GO:0007267 label: cell-cell signaling evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: GDPD2 index: 12 term: id: GO:0030027 label: lamellipodium evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: GFPT2 index: 5 term: id: GO:0006112 label: energy reserve metabolic process evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: GHSR index: 20 term: id: GO:0007565 label: female pregnancy evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: GK5 index: 1 term: id: GO:0005739 label: mitochondrion evidence_type: IBA reference: GO_REF:0000033 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: organelle-root - gene: GK5 index: 15 term: id: GO:0005739 label: mitochondrion evidence_type: HTP reference: PMID:34800366 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: organelle-root - gene: GM2A index: 3 term: id: GO:0009898 label: cytoplasmic side of plasma membrane evidence_type: IBA reference: GO_REF:0000033 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: GM2A index: 13 term: id: GO:0009898 label: cytoplasmic side of plasma membrane evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: GNAS index: 3 term: id: GO:0005886 label: plasma membrane evidence_type: IDA reference: GO_REF:0000052 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: GNB4 index: 17 term: id: GO:0021762 label: substantia nigra development evidence_type: HEP reference: PMID:22926577 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: expression-only - gene: GRAMD1A index: 6 term: id: GO:0005776 label: autophagosome evidence_type: IEA reference: GO_REF:0000044 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: GRAMD1A index: 12 term: id: GO:0031410 label: cytoplasmic vesicle evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: MODIFY rule: general-to-specific replacement_terms: - GO:0005776 autophagosome - gene: GRB2 index: 938 term: id: GO:0045953 label: negative regulation of natural killer cell mediated cytotoxicity evidence_type: IDA reference: PMID:25870599 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_REFERENCE - gene: GTF2F2 index: 23 term: id: GO:0015630 label: microtubule cytoskeleton evidence_type: IDA reference: GO_REF:0000052 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: H3C2 index: 204 term: id: GO:0045296 label: cadherin binding evidence_type: HDA reference: PMID:25468996 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-function - gene: HADHA index: 15 term: id: GO:0052816 label: long-chain fatty acyl-CoA hydrolase activity evidence_type: IDA reference: PMID:22586271 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: HEXA index: 9 term: id: GO:0008375 label: acetylglucosaminyltransferase activity evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: HNF1A index: 13 term: id: GO:0001750 label: photoreceptor outer segment evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: HPRT1 index: 26 term: id: GO:0044209 label: AMP salvage evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: HRAS index: 73 term: id: GO:0043495 label: protein-membrane adaptor activity evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: HSPA1A index: 9 term: id: GO:0046718 label: symbiont entry into host cell evidence_type: IEA reference: GO_REF:0000108 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: HSPA1A index: 11 term: id: GO:0001618 label: virus receptor activity evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: HSPA1A index: 65 term: id: GO:0140545 label: ATP-dependent protein disaggregase activity evidence_type: IDA reference: PMID:23921388 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: HSPA1A index: 190 term: id: GO:0046034 label: ATP metabolic process evidence_type: IDA reference: PMID:23921388 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: HSPA1B index: 9 term: id: GO:0046718 label: symbiont entry into host cell evidence_type: IEA reference: GO_REF:0000108 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: HSPA1B index: 11 term: id: GO:0001618 label: virus receptor activity evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: HSPA1B index: 56 term: id: GO:0140545 label: ATP-dependent protein disaggregase activity evidence_type: IDA reference: PMID:23921388 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: HSPA1B index: 57 term: id: GO:0016887 label: ATP hydrolysis activity evidence_type: IDA reference: PMID:21231916 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: HSPA1B index: 133 term: id: GO:0005814 label: centriole evidence_type: IDA reference: PMID:24061851 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: HSPA1B index: 137 term: id: GO:0034605 label: cellular response to heat evidence_type: IDA reference: PMID:24061851 old_action: REMOVE new_action: ACCEPT rule: ancestor-of-kept - gene: HSPA1B index: 138 term: id: GO:0042026 label: protein refolding evidence_type: IDA reference: PMID:21231916 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: HSPA1B index: 139 term: id: GO:0051082 label: unfolded protein binding evidence_type: IDA reference: PMID:21231916 old_action: REMOVE new_action: MODIFY rule: same-term-kept replacement_terms: - GO:0044183 protein folding chaperone - gene: HSPA1B index: 140 term: id: GO:0070370 label: cellular heat acclimation evidence_type: IMP reference: PMID:21231916 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: same-term-kept - gene: HSPA1B index: 142 term: id: GO:0090084 label: negative regulation of inclusion body assembly evidence_type: IDA reference: PMID:21231916 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: HSPA1B index: 145 term: id: GO:0010628 label: positive regulation of gene expression evidence_type: IMP reference: PMID:25281747 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: ancestor-of-kept - gene: HSPA1B index: 152 term: id: GO:0046034 label: ATP metabolic process evidence_type: IDA reference: PMID:23921388 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: HSPA5 index: 158 term: id: GO:0019899 label: enzyme binding evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: same-term-kept - gene: HSPA5 index: 159 term: id: GO:0019899 label: enzyme binding evidence_type: IPI reference: PMID:23921388 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: HTT index: 12 term: id: GO:0006915 label: apoptotic process evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: MODIFY rule: lateral-correction replacement_terms: - GO:0043066 negative regulation of apoptotic process - gene: IBA57 index: 2 term: id: GO:0006783 label: heme biosynthetic process evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: reason-concedes-truth - gene: IBA57 index: 11 term: id: GO:0003723 label: RNA binding evidence_type: HDA reference: PMID:22681889 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-function - gene: IFT172 index: 12 term: id: GO:0030991 label: intraciliary transport particle A evidence_type: IDA reference: PMID:26980730 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_TERM - gene: IFT52 index: 14 term: id: GO:0030991 label: intraciliary transport particle A evidence_type: IDA reference: PMID:26980730 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_TERM - gene: IFT74 index: 18 term: id: GO:0030991 label: intraciliary transport particle A evidence_type: IDA reference: PMID:26980730 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_TERM - gene: IFT81 index: 23 term: id: GO:0030991 label: intraciliary transport particle A evidence_type: IDA reference: PMID:26980730 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_TERM - gene: IFT88 index: 41 term: id: GO:0030991 label: intraciliary transport particle A evidence_type: IDA reference: PMID:26980730 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_TERM - gene: IL10 index: 66 term: id: GO:0034116 label: positive regulation of heterotypic cell-cell adhesion evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: IL10 index: 67 term: id: GO:0045930 label: negative regulation of mitotic cell cycle evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: IL10 index: 68 term: id: GO:0072577 label: endothelial cell apoptotic process evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: IL10 index: 70 term: id: GO:1904707 label: positive regulation of vascular associated smooth muscle cell proliferation evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: INPP5E index: 32 term: id: GO:0017148 label: negative regulation of translation evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: INTU index: 9 term: id: GO:0005856 label: cytoskeleton evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: INTU index: 31 term: id: GO:0051301 label: cell division evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: INTU index: 32 term: id: GO:0051782 label: negative regulation of cell division evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: IRAK4 index: 118 term: id: GO:0048661 label: positive regulation of smooth muscle cell proliferation evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: IRF3 index: 0 term: id: GO:0000122 label: negative regulation of transcription by RNA polymerase II evidence_type: IEA reference: GO_REF:0000108 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: IRF3 index: 13 term: id: GO:0001227 label: DNA-binding transcription repressor activity, RNA polymerase II-specific evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: IRF3 index: 136 term: id: GO:0019904 label: protein domain specific binding evidence_type: IPI reference: PMID:11583620 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: ITGAM index: 7 term: id: GO:0005178 label: integrin binding evidence_type: NAS reference: PMID:20199584 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: ITGAM index: 100 term: id: GO:0045963 label: negative regulation of dopamine metabolic process evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: ITGAM index: 112 term: id: GO:0160108 label: animal gross anatomical part developmental process evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: ITIH2 index: 10 term: id: GO:0005788 label: endoplasmic reticulum lumen evidence_type: TAS reference: Reactome:R-HSA-8952289 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: er-transit - gene: JAK1 index: 13 term: id: GO:0046872 label: metal ion binding evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: MODIFY rule: general-to-specific replacement_terms: - GO:0000287 magnesium ion binding - gene: JAK1 index: 329 term: id: GO:0005634 label: nucleus evidence_type: IDA reference: PMID:10502458 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: KCNQ1OT1 index: 16 term: id: GO:0005730 label: nucleolus evidence_type: IEA reference: GO_REF:0000115 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: KIF3B index: 52 term: id: GO:0031267 label: small GTPase binding evidence_type: IPI reference: PMID:19635168 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_TERM - gene: KRAS index: 180 term: id: GO:0044877 label: protein-containing complex binding evidence_type: IDA reference: PMID:23209302 old_action: REMOVE new_action: REMOVE rule: remove-rereasoned source_defects: - WRONG_GENE_PRODUCT reason_revised: true - gene: LEPR index: 18 term: id: GO:0007275 label: multicellular organism development evidence_type: TAS reference: PMID:9537324 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: LEPR index: 49 term: id: GO:0048731 label: system development evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: LEPR index: 63 term: id: GO:0160108 label: animal gross anatomical part developmental process evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: LIG4 index: 78 term: id: GO:0006297 label: nucleotide-excision repair, DNA gap filling evidence_type: IBA reference: GO_REF:0000033 old_action: REMOVE new_action: MODIFY rule: same-term-kept replacement_terms: - GO:0006303 double-strand break repair via nonhomologous end joining - gene: LONP1 index: 26 term: id: GO:0042731 label: PH domain binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: LONP1 index: 27 term: id: GO:0043560 label: insulin receptor substrate binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: LONP1 index: 50 term: id: GO:0016020 label: membrane evidence_type: HDA reference: PMID:19946888 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: LONP2 index: 21 term: id: GO:0005634 label: nucleus evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: LONP2 index: 27 term: id: GO:0016020 label: membrane evidence_type: HDA reference: PMID:19946888 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: LPA index: 0 term: id: GO:0004252 label: serine-type endopeptidase activity evidence_type: IEA reference: GO_REF:0000002 old_action: REMOVE new_action: UNDECIDED rule: same-term-kept - gene: LPA index: 1 term: id: GO:0006508 label: proteolysis evidence_type: IEA reference: GO_REF:0000002 old_action: REMOVE new_action: UNDECIDED rule: same-term-kept - gene: LRCH4 index: 13 term: id: GO:0016605 label: PML body evidence_type: IDA reference: PMID:16449650 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: LRP4 index: 41 term: id: GO:0150094 label: amyloid-beta clearance by cellular catabolic process evidence_type: IMP reference: PMID:18289866 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: LRPPRC index: 11 term: id: GO:0006914 label: autophagy evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: reason-concedes-truth - gene: MAML1 index: 63 term: id: GO:0042605 label: peptide antigen binding evidence_type: IPI reference: PMID:17317671 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_TERM - gene: MAP2K1 index: 154 term: id: GO:0032872 label: regulation of stress-activated MAPK cascade evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: MAP7 index: 13 term: id: GO:0005102 label: signaling receptor binding evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: MCL1 index: 77 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-6790041 old_action: REMOVE new_action: MODIFY rule: same-term-kept replacement_terms: - GO:0005737 cytoplasm - gene: MCL1 index: 78 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-9851112 old_action: REMOVE new_action: MODIFY rule: same-term-kept replacement_terms: - GO:0005737 cytoplasm - gene: MCL1 index: 90 term: id: GO:0034097 label: response to cytokine evidence_type: IDA reference: PMID:9184696 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: expression-only - gene: MCL1 index: 111 term: id: GO:1902531 label: regulation of intracellular signal transduction evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: MEX3B index: 11 term: id: GO:0005509 label: calcium ion binding evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: MEX3B index: 12 term: id: GO:0006468 label: protein phosphorylation evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: MEX3B index: 13 term: id: GO:0046777 label: protein autophosphorylation evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: MORC3 index: 6 term: id: GO:0003723 label: RNA binding evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: MTCH2 index: 23 term: id: GO:0005634 label: nucleus evidence_type: HDA reference: PMID:21630459 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: MTIF2 index: 17 term: id: GO:0032790 label: ribosome disassembly evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: MYC index: 57 term: id: GO:0042802 label: identical protein binding evidence_type: IPI reference: PMID:25609649 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: reason-concedes-truth - gene: MYC index: 58 term: id: GO:0042802 label: identical protein binding evidence_type: IPI reference: PMID:9184233 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: reason-concedes-truth - gene: MYD88 index: 122 term: id: GO:0006325 label: chromatin organization evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: MYD88 index: 200 term: id: GO:0048661 label: positive regulation of smooth muscle cell proliferation evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: MYH2 index: 11 term: id: GO:0005911 label: cell-cell junction evidence_type: IMP reference: PMID:25753039 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: NBN index: 222 term: id: GO:0070534 label: protein K63-linked ubiquitination evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_WITH_FROM - gene: NBR1 index: 23 term: id: GO:0005758 label: mitochondrial intermembrane space evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: NDE1 index: 70 term: id: GO:0019904 label: protein domain specific binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: NDUFA9 index: 36 term: id: GO:0005634 label: nucleus evidence_type: HDA reference: PMID:21630459 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: NEUROD1 index: 32 term: id: GO:0005737 label: cytoplasm evidence_type: IEA reference: GO_REF:0000120 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: NID1 index: 11 term: id: GO:0071944 label: cell periphery evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MODIFY rule: lateral-correction replacement_terms: - GO:0005604 basement membrane - gene: NPM1 index: 144 term: id: GO:0005925 label: focal adhesion evidence_type: HDA reference: PMID:21423176 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: NPM1 index: 145 term: id: GO:0016020 label: membrane evidence_type: HDA reference: PMID:19946888 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: OLA1 index: 6 term: id: GO:0005730 label: nucleolus evidence_type: IEA reference: GO_REF:0000120 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: OLA1 index: 17 term: id: GO:0005576 label: extracellular region evidence_type: TAS reference: Reactome:R-HSA-481007 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: OLA1 index: 18 term: id: GO:0031093 label: platelet alpha granule lumen evidence_type: TAS reference: Reactome:R-HSA-481007 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: OLA1 index: 22 term: id: GO:0070062 label: extracellular exosome evidence_type: HDA reference: PMID:19056867 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: OLA1 index: 23 term: id: GO:0070062 label: extracellular exosome evidence_type: HDA reference: PMID:20458337 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: OMA1 index: 20 term: id: GO:0006006 label: glucose metabolic process evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: OMA1 index: 21 term: id: GO:0006006 label: glucose metabolic process evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: OMA1 index: 25 term: id: GO:0006629 label: lipid metabolic process evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: OMA1 index: 26 term: id: GO:0006629 label: lipid metabolic process evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: ORMDL3 index: 19 term: id: GO:0030667 label: secretory granule membrane evidence_type: TAS reference: Reactome:R-HSA-6798743 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: reactome-location - gene: ORMDL3 index: 20 term: id: GO:0035579 label: specific granule membrane evidence_type: TAS reference: Reactome:R-HSA-6799350 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: reactome-location - gene: OTC index: 12 term: id: GO:0005543 label: phospholipid binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: OTC index: 13 term: id: GO:0005743 label: mitochondrial inner membrane evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: PAX6 index: 17 term: id: GO:0050877 label: nervous system process evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: PAX6 index: 44 term: id: GO:0070410 label: co-SMAD binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: PAX6 index: 66 term: id: GO:0001568 label: blood vessel development evidence_type: IMP reference: PMID:7550230 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: experimental-incomplete-evidence - gene: PCSK1 index: 25 term: id: GO:0042802 label: identical protein binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: PCSK1N index: 9 term: id: GO:0005102 label: signaling receptor binding evidence_type: TAS reference: PMID:10632593 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: PDZD7 index: 25 term: id: GO:0005576 label: extracellular region evidence_type: HDA reference: PMID:22664934 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: PEX11A index: 18 term: id: GO:0007165 label: signal transduction evidence_type: IMP reference: PMID:9792670 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: experimental-incomplete-evidence - gene: PEX14 index: 75 term: id: GO:0005634 label: nucleus evidence_type: NAS reference: PMID:11863372 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: reason-concedes-truth - gene: PEX19 index: 54 term: id: GO:0051117 label: ATPase binding evidence_type: IPI reference: PMID:11453642 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: PEX19 index: 72 term: id: GO:0031526 label: brush border membrane evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: PEX2 index: 52 term: id: GO:0016593 label: Cdc73/Paf1 complex evidence_type: IDA reference: PMID:18987311 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: PEX2 index: 53 term: id: GO:0031648 label: protein destabilization evidence_type: IMP reference: PMID:18987311 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: PEX2 index: 54 term: id: GO:0048147 label: negative regulation of fibroblast proliferation evidence_type: IMP reference: PMID:18987311 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: PEX2 index: 55 term: id: GO:0050680 label: negative regulation of epithelial cell proliferation evidence_type: IMP reference: PMID:18987311 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: PEX5 index: 15 term: id: GO:0005794 label: Golgi apparatus evidence_type: IDA reference: GO_REF:0000052 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: organelle-root - gene: PGRMC1 index: 4 term: id: GO:0005576 label: extracellular region evidence_type: IEA reference: GO_REF:0000044 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: PGRMC1 index: 19 term: id: GO:0007613 label: memory evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: PGRMC1 index: 20 term: id: GO:0008306 label: associative learning evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: PGRMC1 index: 26 term: id: GO:0099563 label: modification of synaptic structure evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: PGRMC1 index: 27 term: id: GO:1905809 label: negative regulation of synapse organization evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: PIAS1 index: 131 term: id: GO:0019904 label: protein domain specific binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: PINK1 index: 171 term: id: GO:0044877 label: protein-containing complex binding evidence_type: IMP reference: PMID:24270810 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: PLK1 index: 281 term: id: GO:0019901 label: protein kinase binding evidence_type: IPI reference: PMID:12639966 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: PLK1 index: 282 term: id: GO:0019901 label: protein kinase binding evidence_type: IPI reference: PMID:18615013 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: PLK1 index: 294 term: id: GO:0042802 label: identical protein binding evidence_type: IPI reference: PMID:21041660 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: PLK1 index: 295 term: id: GO:0042802 label: identical protein binding evidence_type: IPI reference: PMID:23354166 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: PLK1 index: 296 term: id: GO:0042802 label: identical protein binding evidence_type: IPI reference: PMID:26192437 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: PLN index: 80 term: id: GO:0010043 label: response to zinc ion evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: PLN index: 100 term: id: GO:0033574 label: response to testosterone evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: PMAIP1 index: 24 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-140214 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: PMAIP1 index: 26 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-140217 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: PMAIP1 index: 39 term: id: GO:0043065 label: positive regulation of apoptotic process evidence_type: IMP reference: PMID:21525171 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: PMAIP1 index: 45 term: id: GO:0071456 label: cellular response to hypoxia evidence_type: IEP reference: PMID:20810912 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept source_defects: - WRONG_REFERENCE - gene: PMAIP1 index: 47 term: id: GO:0072593 label: reactive oxygen species metabolic process evidence_type: IDA reference: PMID:14699081 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: downstream-readout - gene: PMPCA index: 22 term: id: GO:0005576 label: extracellular region evidence_type: HDA reference: PMID:22664934 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: PPP2R2A index: 65 term: id: GO:0044877 label: protein-containing complex binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MODIFY rule: general-to-specific replacement_terms: - GO:0048156 tau protein binding - gene: PRG2 index: 14 term: id: GO:0031012 label: extracellular matrix evidence_type: HDA reference: PMID:28344315 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: PRG2 index: 16 term: id: GO:0031012 label: extracellular matrix evidence_type: HDA reference: PMID:25037231 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: PRG2 index: 19 term: id: GO:0070062 label: extracellular exosome evidence_type: HDA reference: PMID:23533145 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: PRG3 index: 3 term: id: GO:0031012 label: extracellular matrix evidence_type: HDA reference: PMID:28344315 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: PRG3 index: 5 term: id: GO:0031012 label: extracellular matrix evidence_type: HDA reference: PMID:25037231 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: PRG3 index: 11 term: id: GO:0017148 label: negative regulation of translation evidence_type: IDA reference: PMID:10318872 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: PRRT1 index: 14 term: id: GO:0006468 label: protein phosphorylation evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: PSMA1 index: 33 term: id: GO:0001530 label: lipopolysaccharide binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: PTCH1 index: 63 term: id: GO:0044877 label: protein-containing complex binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: PTEN index: 22 term: id: GO:0010604 label: positive regulation of macromolecule metabolic process evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: PTPRC index: 62 term: id: GO:0010332 label: response to gamma radiation evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: PYCARD index: 4 term: id: GO:0002020 label: protease binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: PYCARD index: 109 term: id: GO:0008385 label: IkappaB kinase complex evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: PYCARD index: 164 term: id: GO:0044325 label: transmembrane transporter binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: RAD21 index: 120 term: id: GO:0016020 label: membrane evidence_type: HDA reference: PMID:19946888 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: RAD21 index: 127 term: id: GO:0032691 label: negative regulation of interleukin-1 beta production evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: RAD21 index: 128 term: id: GO:0032720 label: negative regulation of tumor necrosis factor production evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: RAD21 index: 129 term: id: GO:0032733 label: positive regulation of interleukin-10 production evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: RAD21 index: 132 term: id: GO:0034351 label: negative regulation of glial cell apoptotic process evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: RAD21 index: 133 term: id: GO:0043524 label: negative regulation of neuron apoptotic process evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: RAD21 index: 137 term: id: GO:0106222 label: lncRNA binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: RARA index: 138 term: id: GO:0005102 label: signaling receptor binding evidence_type: IDA reference: PMID:19628791 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: RASA3 index: 4 term: id: GO:0006950 label: response to stress evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: RASAL3 index: 15 term: id: GO:0070062 label: extracellular exosome evidence_type: HDA reference: PMID:20458337 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: RB1 index: 182 term: id: GO:0007265 label: Ras protein signal transduction evidence_type: IEP reference: PMID:9054499 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: expression-only - gene: RB1 index: 189 term: id: GO:0031625 label: ubiquitin protein ligase binding evidence_type: IPI reference: PMID:10944455 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: RBX1 index: 423 term: id: GO:0061629 label: RNA polymerase II-specific DNA-binding transcription factor binding evidence_type: IPI reference: PMID:14739464 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: reason-concedes-truth - gene: RDH5 index: 13 term: id: GO:0044297 label: cell body evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: RDH8 index: 5 term: id: GO:0006694 label: steroid biosynthetic process evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: RFXANK index: 2 term: id: GO:0003677 label: DNA binding evidence_type: IEA reference: GO_REF:0000043 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: reason-concedes-truth - gene: RFXANK index: 16 term: id: GO:0000977 label: RNA polymerase II transcription regulatory region sequence-specific DNA binding evidence_type: IDA reference: PMID:9806546 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: RFXAP index: 2 term: id: GO:0003677 label: DNA binding evidence_type: IEA reference: GO_REF:0000120 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: reason-concedes-truth - gene: RPL18A index: 19 term: id: GO:0006941 label: striated muscle contraction evidence_type: NAS reference: PMID:34081545 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: RPL18A index: 23 term: id: GO:1901740 label: negative regulation of myoblast fusion evidence_type: NAS reference: PMID:26684695 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: RPS3 index: 11 term: id: GO:0005743 label: mitochondrial inner membrane evidence_type: IEA reference: GO_REF:0000044 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: same-term-kept - gene: RSL1D1 index: 0 term: id: GO:0001649 label: osteoblast differentiation evidence_type: HDA reference: PMID:16210410 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: expression-only - gene: SAMM50 index: 25 term: id: GO:0070062 label: extracellular exosome evidence_type: HDA reference: PMID:19056867 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: SCGB1A1 index: 0 term: id: GO:0005737 label: cytoplasm evidence_type: IBA reference: GO_REF:0000033 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: SCGB1A1 index: 13 term: id: GO:0000122 label: negative regulation of transcription by RNA polymerase II evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: SCGB1A1 index: 15 term: id: GO:0005635 label: nuclear envelope evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: er-transit - gene: SCGB1A1 index: 28 term: id: GO:0043488 label: regulation of mRNA stability evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: SCGB2A2 index: 1 term: id: GO:0030521 label: androgen receptor signaling pathway evidence_type: IBA reference: GO_REF:0000033 old_action: REMOVE new_action: UNDECIDED rule: iba-node-not-examined - gene: SCN1A index: 20 term: id: GO:0014704 label: intercalated disc evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: SCN1A index: 24 term: id: GO:0030018 label: Z disc evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: SCN1A index: 25 term: id: GO:0030315 label: T-tubule evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: SCN1A index: 49 term: id: GO:0030018 label: Z disc evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: SCN9A index: 16 term: id: GO:0007623 label: circadian rhythm evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: SCP2 index: 51 term: id: GO:0005102 label: signaling receptor binding evidence_type: IPI reference: PMID:21375735 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_TERM reason_revised: true - gene: SDHA index: 36 term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence_type: NAS reference: PMID:30030361 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: cross-gene-consistency - gene: SDHB index: 29 term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence_type: NAS reference: PMID:30030361 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: cross-gene-consistency - gene: SDHC index: 15 term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence_type: NAS reference: PMID:30030361 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: cross-gene-consistency - gene: SERP1 index: 9 term: id: GO:0005881 label: cytoplasmic microtubule evidence_type: IDA reference: PMID:23264731 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: SGCA index: 15 term: id: GO:0005911 label: cell-cell junction evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: SGCA index: 17 term: id: GO:0045121 label: membrane raft evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: SIRT1 index: 206 term: id: GO:0051658 label: maintenance of nucleus location evidence_type: IDA reference: PMID:15692560 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: SIRT1 index: 211 term: id: GO:0160012 label: histone decrotonylase activity, NAD-dependent evidence_type: IDA reference: PMID:28497810 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: promiscuous-activity - gene: SIRT1 index: 224 term: id: GO:0007179 label: transforming growth factor beta receptor signaling pathway evidence_type: IDA reference: PMID:23960241 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: expression-only - gene: SIRT1 index: 243 term: id: GO:0001938 label: positive regulation of endothelial cell proliferation evidence_type: IMP reference: PMID:20203304 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: SIRT1 index: 248 term: id: GO:0016922 label: nuclear receptor binding evidence_type: IPI reference: PMID:24043310 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: experimental-incomplete-evidence - gene: SIRT1 index: 256 term: id: GO:1990254 label: keratin filament binding evidence_type: IPI reference: PMID:23382074 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-function - gene: SIRT1 index: 275 term: id: GO:1902176 label: negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway evidence_type: IMP reference: PMID:17317627 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: experimental-incomplete-evidence - gene: SIRT1 index: 289 term: id: GO:2000481 label: positive regulation of cAMP-dependent protein kinase activity evidence_type: IMP reference: PMID:18687677 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: SIRT1 index: 291 term: id: GO:2000774 label: positive regulation of cellular senescence evidence_type: IDA reference: PMID:18687677 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: SIRT1 index: 300 term: id: GO:0000012 label: single strand break repair evidence_type: IMP reference: PMID:20097625 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: SIRT1 index: 312 term: id: GO:0007346 label: regulation of mitotic cell cycle evidence_type: IDA reference: PMID:15692560 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: SIRT2 index: 60 term: id: GO:0005739 label: mitochondrion evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: organelle-root - gene: SIRT2 index: 88 term: id: GO:0005739 label: mitochondrion evidence_type: HTP reference: PMID:34800366 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: organelle-root - gene: SIRT2 index: 99 term: id: GO:0140297 label: DNA-binding transcription factor binding evidence_type: IPI reference: PMID:15126506 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: SIRT2 index: 100 term: id: GO:0003950 label: NAD+ poly-ADP-ribosyltransferase activity evidence_type: IDA reference: PMID:10381378 old_action: REMOVE new_action: REMOVE rule: remove-rereasoned reason_revised: true - gene: SIX3 index: 30 term: id: GO:0007601 label: visual perception evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: SIX6 index: 12 term: id: GO:0007601 label: visual perception evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: SNCA index: 259 term: id: GO:0005840 label: ribosome evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: SPHK1 index: 5 term: id: GO:0003376 label: sphingosine-1-phosphate receptor signaling pathway evidence_type: IEA reference: GO_REF:0000108 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: SPHK1 index: 15 term: id: GO:0038036 label: sphingosine-1-phosphate receptor activity evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: SPHK2 index: 13 term: id: GO:0038036 label: sphingosine-1-phosphate receptor activity evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: SPOCK1 index: 18 term: id: GO:0005737 label: cytoplasm evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: er-transit - gene: SPOCK1 index: 25 term: id: GO:0016528 label: sarcoplasm evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: er-transit - gene: SPR index: 16 term: id: GO:0008106 label: alcohol dehydrogenase (NADP+) activity evidence_type: TAS reference: PMID:1883349 old_action: REMOVE new_action: MODIFY rule: general-to-specific replacement_terms: - GO:0004757 sepiapterin reductase (NADP+) activity - gene: SRD5A3 index: 8 term: id: GO:0047751 label: 3-oxo-5-alpha-steroid 4-dehydrogenase (NADP+) activity evidence_type: IEA reference: GO_REF:0000120 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: SREBF2 index: 8 term: id: GO:0000247 label: C-8 sterol isomerase activity evidence_type: IDA reference: PMID:12941800 negated: true old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: SRPRB index: 13 term: id: GO:0005881 label: cytoplasmic microtubule evidence_type: IDA reference: PMID:23264731 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: SSR2 index: 6 term: id: GO:0031204 label: post-translational protein targeting to membrane, translocation evidence_type: NAS reference: PMID:36697828 old_action: REMOVE new_action: MODIFY rule: lateral-correction replacement_terms: - GO:0006613 cotranslational protein targeting to membrane - gene: ST3GAL5 index: 4 term: id: GO:0009101 label: glycoprotein biosynthetic process evidence_type: IEA reference: GO_REF:0000002 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: STAT1 index: 40 term: id: GO:0031730 label: CCR5 chemokine receptor binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: STAT1 index: 42 term: id: GO:0051721 label: protein phosphatase 2A binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: STAT1 index: 54 term: id: GO:0045296 label: cadherin binding evidence_type: HDA reference: PMID:25468996 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-function - gene: STAT1 index: 178 term: id: GO:0030424 label: axon evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: STAT1 index: 179 term: id: GO:0030425 label: dendrite evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: STEAP2 index: 12 term: id: GO:0009725 label: response to hormone evidence_type: IDA reference: PMID:12095985 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: expression-only - gene: STING1 index: 49 term: id: GO:0005777 label: peroxisome evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: organelle-root - gene: SYN2 index: 11 term: id: GO:0014069 label: postsynaptic density evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: SYN3 index: 13 term: id: GO:0014069 label: postsynaptic density evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: SYP index: 31 term: id: GO:2000474 label: regulation of opioid receptor signaling pathway evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: SYVN1 index: 26 term: id: GO:0005886 label: plasma membrane evidence_type: IDA reference: GO_REF:0000052 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: TERT index: 46 term: id: GO:0005886 label: plasma membrane evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: TFAP2A index: 34 term: id: GO:0005515 label: protein binding evidence_type: IPI reference: PMID:11447109 old_action: REMOVE new_action: REMOVE rule: protein-binding-audit source_defects: - WRONG_GENE_PRODUCT - gene: TFAP2B index: 0 term: id: GO:0000122 label: negative regulation of transcription by RNA polymerase II evidence_type: IDA reference: PMID:7559606 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: TFAP2B index: 10 term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific evidence_type: IDA reference: PMID:7559606 old_action: REMOVE new_action: ACCEPT rule: same-term-kept source_defects: - WRONG_REFERENCE - gene: TFRC index: 27 term: id: GO:0030544 label: Hsp70 protein binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: TFRC index: 31 term: id: GO:0051087 label: protein-folding chaperone binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: TFRC index: 59 term: id: GO:0007166 label: cell surface receptor signaling pathway evidence_type: IDA reference: PMID:9465039 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: reason-concedes-truth - gene: THBS2 index: 11 term: id: GO:0051965 label: positive regulation of synapse assembly evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: TIMM50 index: 24 term: id: GO:0005134 label: interleukin-2 receptor binding evidence_type: IDA reference: PMID:15044455 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_TERM - gene: TLR2 index: 132 term: id: GO:0051607 label: defense response to virus evidence_type: IEP reference: PMID:32634389 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: expression-only - gene: TLR9 index: 96 term: id: GO:0034165 label: positive regulation of toll-like receptor 9 signaling pathway evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MODIFY rule: lateral-correction replacement_terms: - GO:0034162 toll-like receptor 9 signaling pathway - gene: TOLLIP index: 71 term: id: GO:0016310 label: phosphorylation evidence_type: IDA reference: PMID:1085432 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_REFERENCE - gene: TOMM70 index: 17 term: id: GO:0061052 label: negative regulation of cell growth involved in cardiac muscle cell development evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: TOMM70 index: 55 term: id: GO:0070062 label: extracellular exosome evidence_type: HDA reference: PMID:18570454 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-location - gene: TP53 index: 23 term: id: GO:0008283 label: cell population proliferation evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: TOO_GENERAL rule: ancestor-of-kept - gene: TP53 index: 27 term: id: GO:0009651 label: response to salt stress evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: TP53 index: 56 term: id: GO:0048144 label: fibroblast proliferation evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: TP53 index: 60 term: id: GO:0051276 label: chromosome organization evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: TP53 index: 70 term: id: GO:0072089 label: stem cell proliferation evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: TP53 index: 444 term: id: GO:0031625 label: ubiquitin protein ligase binding evidence_type: IEA reference: GO_REF:0000120 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: TP53 index: 521 term: id: GO:0031625 label: ubiquitin protein ligase binding evidence_type: EXP reference: PMID:8875929 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: TP53 index: 831 term: id: GO:0031625 label: ubiquitin protein ligase binding evidence_type: IPI reference: PMID:8875929 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reason-concedes-truth - gene: TRAF2 index: 664 term: id: GO:0043120 label: tumor necrosis factor binding evidence_type: IPI reference: PMID:23429285 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_TERM - gene: TRAF6 index: 176 term: id: GO:0005811 label: lipid droplet evidence_type: IEA reference: GO_REF:0000120 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: TRAF6 index: 293 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-177690 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 294 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-177692 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 295 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-450259 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 296 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-450358 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 297 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-847070 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 298 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-9628444 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 299 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-9685219 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 300 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975097 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 301 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975103 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 302 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975147 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 305 term: id: GO:0005811 label: lipid droplet evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: TRAF6 index: 382 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-177694 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 383 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975100 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 384 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975106 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 385 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975111 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 386 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975118 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 387 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975119 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 388 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975122 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 389 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975139 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 390 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975142 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 391 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975185 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TRAF6 index: 392 term: id: GO:0010008 label: endosome membrane evidence_type: TAS reference: Reactome:R-HSA-975188 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: reactome-location - gene: TUSC3 index: 6 term: id: GO:0015095 label: magnesium ion transmembrane transporter activity evidence_type: IEA reference: GO_REF:0000117 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: same-term-kept - gene: TXN index: 54 term: id: GO:0047134 label: protein-disulfide reductase [NAD(P)H] activity evidence_type: IDA reference: PMID:17182577 old_action: REMOVE new_action: MODIFY rule: lateral-correction replacement_terms: - GO:0015035 protein-disulfide reductase activity - gene: UMPS index: 12 term: id: GO:0006225 label: UDP biosynthetic process evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: UMPS index: 13 term: id: GO:0044210 label: '''de novo'' CTP biosynthetic process' evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: UROS index: 7 term: id: GO:0005542 label: folic acid binding evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: USO1 index: 0 term: id: GO:0045056 label: transcytosis evidence_type: IBA reference: GO_REF:0000033 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: USO1 index: 21 term: id: GO:0032252 label: secretory granule localization evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: USO1 index: 23 term: id: GO:1900076 label: regulation of cellular response to insulin stimulus evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: KEEP_AS_NON_CORE rule: claim-established - gene: USO1 index: 26 term: id: GO:0045296 label: cadherin binding evidence_type: HDA reference: PMID:25468996 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-function - gene: USO1 index: 42 term: id: GO:0003723 label: RNA binding evidence_type: HDA reference: PMID:22658674 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: omics-function - gene: USP25 index: 21 term: id: GO:0016071 label: mRNA metabolic process evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: USP25 index: 23 term: id: GO:0065003 label: protein-containing complex assembly evidence_type: IEA reference: GO_REF:0000107 old_action: REMOVE new_action: MARK_AS_OVER_ANNOTATED rule: electronic-unsupported-plausible - gene: VAPA index: 162 term: id: GO:0044828 label: host-mediated suppression of viral genome replication evidence_type: IDA reference: PMID:19515777 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_GENE_PRODUCT - gene: VTI1A index: 37 term: id: GO:0050882 label: voluntary musculoskeletal movement evidence_type: IMP reference: PMID:22958904 old_action: REMOVE new_action: UNDECIDED rule: experimental-incomplete-evidence - gene: WT1 index: 53 term: id: GO:0045893 label: positive regulation of DNA-templated transcription evidence_type: IDA reference: PMID:9178767 old_action: REMOVE new_action: ACCEPT rule: same-term-kept source_defects: - WRONG_GENE_PRODUCT - gene: WT1 index: 75 term: id: GO:0045893 label: positive regulation of DNA-templated transcription evidence_type: IDA reference: PMID:12802290 old_action: REMOVE new_action: ACCEPT rule: same-term-kept - gene: WT1 index: 104 term: id: GO:0007356 label: thorax and anterior abdomen determination evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: REMOVE rule: source-defect-recorded source_defects: - WRONG_TERM - gene: WT1 index: 122 term: id: GO:0043010 label: camera-type eye development evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: MODIFY rule: general-to-specific replacement_terms: - GO:0060041 retina development in camera-type eye - gene: ZP3 index: 52 term: id: GO:0045892 label: negative regulation of DNA-templated transcription evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: REMOVE rule: remove-rereasoned reason_revised: true - gene: ZP3 index: 53 term: id: GO:0045893 label: positive regulation of DNA-templated transcription evidence_type: ISS reference: GO_REF:0000024 old_action: REMOVE new_action: REMOVE rule: remove-rereasoned reason_revised: true consistency_followups: - gene: ADGRA2 index: 58 term: id: GO:0016020 label: membrane evidence_type: TAS reference: PMID:15203201 old_action: KEEP_AS_NON_CORE new_action: KEEP_AS_NON_CORE rule: same-term-kept - gene: HSPA1B index: 16 term: id: GO:0005814 label: centriole evidence_type: IEA reference: GO_REF:0000117 old_action: MARK_AS_OVER_ANNOTATED new_action: ACCEPT rule: same-term-kept retained_with_note: - gene: ABCB6 index: 51 term: id: GO:0007420 label: brain development evidence_type: IMP reference: PMID:22100072 note: Full text of PMID:22100072 (ELOVL4 paper) does not mention ABCB6; possibly a mis-keyed reference; recorded as a source defect - gene: ACAT1 index: 16 term: id: GO:0034736 label: cholesterol O-acyltransferase activity evidence_type: IDA reference: PMID:32944968 note: Paper's 'ACAT' is SOAT-type cholesterol acyltransferase; first reviewer read full text; ACAT1 (P24752) is a thiolase - gene: ADAM17 index: 147 term: id: GO:0043130 label: ubiquitin binding evidence_type: IMP reference: PMID:38771644 note: 'Full text: ADAM17 binds E3 ligase TRIM47 and is ubiquitinated; no ubiquitin-binding assay. Term slip for ubiquitin protein ligase binding possible' - gene: AIP index: 22 term: id: GO:0003755 label: peptidyl-prolyl cis-trans isomerase activity evidence_type: IDA reference: PMID:14557246 note: 'Full text of PMID:14557246 checked: PPIase appears only as a domain name; no isomerase assay; chaperone-like holdase shown' - gene: ALDOB index: 46 term: id: GO:0070061 label: fructose binding evidence_type: IMP reference: PMID:10625657 close_call: true note: IMP 'fructose binding' on abstract-only paper; removal rests on GO definition (free fructose) vs phosphorylated substrates; REMOVE stands - gene: APEX1 index: 47 term: id: GO:0033892 label: deoxyribonuclease (pyrimidine dimer) activity evidence_type: IDA reference: PMID:19188445 close_call: true note: Two IDA rows to pyrimidine-dimer DNase; abstracts describe AP-endonuclease assays; MODIFY to GO:0003906 would be an alternative, claim as stated is false - gene: APOO index: 2 term: id: GO:0001401 label: SAM complex evidence_type: HDA reference: PMID:26477565 note: 'SAM complex HDA: correct complex (MIB complex GO:0140275, same reference) is ACCEPTed in the review; REMOVE of the outer-membrane complex term stands' - gene: ARPP19 index: 6 term: id: GO:0005102 label: signaling receptor binding evidence_type: IDA reference: PMID:9653196 note: 'Full text: assays used alpha-endosulfine (ENSA), stated to be a different gene; recorded as a source defect' - gene: ATAD1 index: 23 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-9603775 close_call: true note: Reactome cytosol rows for a membrane-anchored protein reflect PEX19-bound targeting intermediate; REMOVE stands - gene: BACH1 index: 73 term: id: GO:0006281 label: DNA repair evidence_type: IMP reference: PMID:11301010 note: Symbol collision stated in abstract (BACH1 helicase = BRIP1); recorded as a source defect - gene: BAX index: 129 term: id: GO:0005757 label: mitochondrial permeability transition pore complex evidence_type: IDA reference: PMID:9843949 close_call: true note: MPTP-complex IDA (abstract-only) removed as a superseded model; MARK_AS_OVER_ANNOTATED would be an alternative - gene: BNIP3L index: 63 term: id: GO:0051607 label: defense response to virus evidence_type: IDA reference: PMID:9973195 close_call: true note: IDA defense response to virus; abstract shows E1B-19K interaction/antagonism; later literature shows viral exploitation of NIX; REMOVE stands - gene: CALCOCO2 index: 35 term: id: GO:0034341 label: response to type II interferon evidence_type: IDA reference: PMID:9230084 close_call: true note: Full text says IFN-gamma only marginally enhances NDP52; removal defensible - gene: CD4 index: 107 term: id: GO:0019865 label: immunoglobulin binding evidence_type: IEA reference: GO_REF:0000107 note: 'Donor paper (PMID:2338715) is crystallization of rat CD4 with an antibody Fab: antigen-antibody complex, not Ig-binding function; REMOVE stands' - gene: CDO1 index: 7 term: id: GO:0007595 label: lactation evidence_type: IEA reference: GO_REF:0000107 note: '7 rodent ''response to X''/lactation rows: donors are IDA of enzyme-activity changes under physiological/hormonal conditions (regulation of the enzyme, not participation in the response); REMOVE stands' - gene: CKM index: 17 term: id: GO:0005576 label: extracellular region evidence_type: IEA reference: GO_REF:0000107 close_call: true note: Donor IDA (PMID:24177035) is serum CK as a muscle-damage marker; leakage rather than a location; CKB's parallel ISS row is MARK_AS_OVER_ANNOTATED - gene: COP1 index: 11 term: id: GO:0000139 label: Golgi membrane evidence_type: IEA reference: GO_REF:0000107 note: 'Donor paper (PMID:15147909) is about ARF/coatomer (COPI) on Golgi membranes: rat ''Cop1'' annotation is a coatomer/COP1 symbol collision at source; REMOVE stands; recorded as a source defect' - gene: CRY1 index: 5 term: id: GO:0043153 label: entrainment of circadian clock by photoperiod evidence_type: IBA reference: GO_REF:0000033 close_call: true note: Entrainment/response-to-light rows (IBA, IEA, ISS; mouse IMP donors on SCN clockwork and retinal clock) removed on the lineage argument that mammalian cryptochromes are light-independent; REMOVE stands; a curator may prefer MARK_AS_OVER_ANNOTATED - gene: CRY2 index: 43 term: id: GO:0009416 label: response to light stimulus evidence_type: IMP reference: PMID:15751956 close_call: true note: IMP response to light stimulus (PMID:15751956, abstract-only; paper analysed C-terminal domains of Arabidopsis Cry1 and a human cryptochrome); removal rests on the established light-independence of mammalian CRY2 - gene: CRY2 index: 57 term: id: GO:0005576 label: extracellular region evidence_type: IDA reference: PMID:9753616 note: Two IDA rows cite the STC2 cloning paper (PMID:9753616); terms match stanniocalcin-2 biology, not CRY2; REMOVE stands; recorded as a source defect - gene: CYB5R4 index: 16 term: id: GO:0046677 label: response to antibiotic evidence_type: ISS reference: GO_REF:0000024 close_call: true note: Donor IMP (PMID:17343567, NCB5OR redox/ER-stress study in beta cells); 'response to antibiotic' probably reflects tunicamycin/streptozotocin treatment; REMOVE stands - gene: DPEP1 index: 41 term: id: GO:0071277 label: cellular response to calcium ion evidence_type: ISS reference: GO_REF:0000024 note: 'Donors (pig/rat DPEP1 IDA) describe Ca2+- and NO-regulated release of the GPI-anchored enzyme: DPEP1 is the regulated cargo, not a participant in the response; REMOVE defensible' - gene: DPYS index: 9 term: id: GO:0051219 label: phosphoprotein binding evidence_type: IEA reference: GO_REF:0000107 close_call: true note: Donor is rat Dpys IPI from the CRMP5 characterization paper (PMID:10956643); possible real DHPase-CRMP interaction or family mis-assignment; REMOVE stands - gene: EFEMP1 index: 71 term: id: GO:0043010 label: camera-type eye development evidence_type: IEP reference: PMID:25406291 note: Fibrillin-3 (FBN3) vs fibulin-3 (EFEMP1) name collision, explicit in title; three IEP rows; recorded as a source defect - gene: ELOB index: 57 term: id: GO:0006367 label: transcription initiation at RNA polymerase II promoter evidence_type: IDA reference: PMID:7660122 note: IDA to transcription initiation from a paper on VHL inhibition of transcription elongation (title-explicit); elongation is annotated elsewhere; REMOVE stands (same for ELOC[68]) - gene: ERCC4 index: 38 term: id: GO:0061819 label: telomeric DNA-containing double minutes formation evidence_type: IMP reference: PMID:14690602 close_call: true note: IMP to TDM formation although the paper's title says ERCC1/XPF represses formation; no negative-regulation term exists in GO; REMOVE stands - gene: FADS1 index: 22 term: id: GO:0016213 label: acyl-CoA 6-desaturase activity evidence_type: IDA reference: PMID:10601301 close_call: true note: IDA to acyl-CoA 6-desaturase from the delta-5 desaturase cloning paper (abstract-only); abstract states the expressed ORF converts 20:3(n-6) to 20:4(n-6), i.e. delta-5; delta-5 IDA exists from PMID:10769175; REMOVE stands as a contradicted activity (MODIFY to GO:0062076 would be an alternative) - gene: FADS1 index: 30 term: id: GO:0009267 label: cellular response to starvation evidence_type: IDA reference: PMID:10601301 close_call: true note: IDA to cellular response to starvation; abstract describes rat liver mRNA lower on PUFA diets than on fat-free diet, i.e. dietary regulation of expression, not starvation; REMOVE stands - gene: FASLG index: 110 term: id: GO:0048388 label: endosomal lumen acidification evidence_type: IEA reference: GO_REF:0000107 note: 'Donor rat Faslg IDA (PMID:18045865): CD95L added to hepatocytes triggers endosomal acidification in the responding cell; ligand as stimulus, not participant; REMOVE stands' - gene: FGF23 index: 160 term: id: GO:0005737 label: cytoplasm evidence_type: IBA reference: GO_REF:0000033 note: IBA is_active_in cytoplasm on a secreted FGF; kept ER/Golgi lumen rows are located_in transit locations and do not entail activity in the cytoplasm; REMOVE stands (same for FGF7[51], FGF10[91], FGF19[41], FGF21[18]) - gene: FUT8 index: 23 term: id: GO:0036066 label: protein O-linked glycosylation via fucose evidence_type: IEA reference: GO_REF:0000108 note: O-fucosylation inferred through a GO part_of edge from the core-fucosyltransferase activity; FUT8 fucosylates N-glycan core GlcNAc, so the claim is false and the edge is an ontology problem; REMOVE stands; recorded as a source defect - gene: GATA4 index: 74 term: id: GO:0009410 label: response to xenobiotic stimulus evidence_type: IMP reference: PMID:20585342 close_call: true note: IMP to response to xenobiotic stimulus from a pharmacogenetic association of an intronic GATA4 SNP with relapse under acamprosate (abstract states the design); association is not participation; REMOVE stands - gene: GCNT1 index: 16 term: id: GO:0016607 label: nuclear speck evidence_type: IDA reference: GO_REF:0000052 close_call: true note: HPA immunofluorescence nuclear speck on a type II Golgi membrane enzyme with a lumenal catalytic domain; topological contradiction argued in the reason; REMOVE stands although HPA rows are otherwise re-actioned to MARK_AS_OVER_ANNOTATED - gene: GDPD2 index: 2 term: id: GO:0005737 label: cytoplasm evidence_type: IEA reference: GO_REF:0000044 close_call: true note: Cytoplasm IEA from UniProt By-similarity location on a multi-pass plasma-membrane protein; removal argued on topology; REMOVE stands - gene: GMFG index: 13 term: id: GO:0004860 label: protein kinase inhibitor activity evidence_type: TAS reference: PMID:8639570 note: TAS rows cite 1995-1996 papers on brain GMF (GMF-beta), which predate the description of GMF-gamma; REMOVE stands; not structured as a source defect - gene: GNAS index: 6 term: id: GO:0005634 label: nucleus evidence_type: IDA reference: PMID:20862257 note: 'IDA nucleus from the neuroblastoma NESP55 study (full text cached): NESP55 staining described in soma and processes; ''nuclear'' in the text refers to counterstain and HIF2-alpha; REMOVE stands' - gene: GRPEL1 index: 19 term: id: GO:0051082 label: unfolded protein binding evidence_type: IDA reference: PMID:11311562 close_call: true note: IDA unfolded protein binding (obsolete term) on a nucleotide exchange factor from an abstract-only paper; removal follows the unfolded-protein-binding policy that co-chaperones acting on Hsp70 are not substrate binders; REMOVE stands - gene: HNF1A index: 13 term: id: GO:0001750 label: photoreceptor outer segment evidence_type: IEA reference: GO_REF:0000107 note: Donor mouse Hnf1a IGI cites PMID:10090727, a Lef1/Tcf1 (Tcf7) double-mutant paper; HNF1A's former symbol TCF1 collides with Tcf1; REMOVE stands; recorded as a source defect - gene: HSPA1L index: 31 term: id: GO:0006986 label: response to unfolded protein evidence_type: TAS reference: PMID:9685725 close_call: true note: TAS response to unfolded protein from a genomic-structure paper; HSPA1L is constitutively expressed in testis and not stress-induced; chaperone activity is annotated elsewhere; REMOVE stands - gene: HTT index: 74 term: id: GO:0031648 label: protein destabilization evidence_type: IMP reference: PMID:17947297 close_call: true note: IMP protein destabilization and IDA positive regulation of apoptosis ([76]) from the HYPK study of N-terminal huntingtin with 40 glutamines (abstract-only; system explicit in title); annotations reflect the pathogenic fragment, not normal HTT function; REMOVE stands - gene: IRAK3 index: 0 term: id: GO:0000287 label: magnesium ion binding evidence_type: IDA reference: PMID:10383454 close_call: true note: IDA magnesium binding and kinase activity (PMID:10383454, abstract-only) on a pseudokinase; contradicted by the IRAK3 structure (DFG to DFA, HRD to CGS, no Mg/ATP stabilisation) and the 1999 report's own 'negligible autophosphorylation'; REMOVE stands as a contradicted function - gene: IRAK4 index: 40 term: id: GO:0005576 label: extracellular region evidence_type: IEA reference: GO_REF:0000107 close_call: true note: Donor rat Irak4 IDA extracellular region from a sepsis pharmacology study (PMID:23073793) that measures IRAK-4 in liver; cytosolic kinase without signal peptide; REMOVE stands - gene: KIF3B index: 52 term: id: GO:0031267 label: small GTPase binding evidence_type: IPI reference: PMID:19635168 note: IPI small GTPase binding whose recorded partner ARHGEF10 is a RhoGEF, not a GTPase; REMOVE stands; recorded as a source defect - gene: LCMT1 index: 20 term: id: GO:0090266 label: regulation of mitotic cell cycle spindle assembly checkpoint evidence_type: IMP reference: PMID:17724024 close_call: true note: IMP (acts_upstream_of_or_within) and its IBA on spindle assembly checkpoint regulation; removal re-interprets the paper's nocodazole data with a comparator check and is the subject of an upstream ticket (go-annotation#6632); REMOVE stands as a deliberate, tracked decision; recorded as a source defect - gene: LEP index: 28 term: id: GO:0005829 label: cytosol evidence_type: IEA reference: GO_REF:0000107 close_call: true note: Cytosol transferred from rat Lep IDA (PMID:17324488); secreted hormone with signal peptide, so intracellular staining reflects the secretory pathway; REMOVE stands on topology - gene: LPCAT4 index: 26 term: id: GO:0003841 label: 1-acylglycerol-3-phosphate O-acyltransferase activity evidence_type: TAS reference: Reactome:R-HSA-75885 note: Same GO term is MODIFY on other Reactome rows (other lysophospholipid events); this event is specifically LPA acylation, contradicted by direct biochemistry (PMID:18458083); REMOVE stands (also [28], position-specific LPG event) - gene: LRAT index: 13 term: id: GO:0001972 label: retinoic acid binding evidence_type: IEA reference: GO_REF:0000107 note: Donor rat Lrat IDA rows cite studies of retinoic acid inducing hepatic LRAT activity (PMID:8460936, PMID:9244401), i.e. regulation by retinoic acid, not binding; REMOVE stands - gene: LRRC32 index: 6 term: id: GO:0005654 label: nucleoplasm evidence_type: IDA reference: GO_REF:0000052 close_call: true note: HPA nucleoplasm on a type I plasma-membrane protein with signal peptide and extracellular LRR domain; topological contradiction; REMOVE stands - gene: MBL2 index: 40 term: id: GO:0006508 label: proteolysis evidence_type: IDA reference: PMID:22691502 close_call: true note: IDA proteolysis on the recognition subunit of MBL-MASP complexes; MASPs perform the cleavage; lectin-pathway and complex-membership rows are kept; REMOVE stands - gene: MDH2 index: 12 term: id: GO:0016020 label: membrane evidence_type: IEA reference: GO_REF:0000107 close_call: true note: Membrane IEA from mouse Mdh2 (inner-membrane proteome HDA and an IMP); soluble matrix enzyme; REMOVE stands - gene: MORC3 index: 34 term: id: GO:0006468 label: protein phosphorylation evidence_type: IDA reference: PMID:17332504 close_call: true note: IDA rows (acts_upstream_of_or_within) to phosphorylation and protein stabilization from the MORC3-p53 study; full text states that stress-induced p53 phosphorylation and stabilization still occur in Morc3-deficient fibroblasts; REMOVE stands ([34],[36],[38]) - gene: MS4A1 index: 1 term: id: GO:0005154 label: epidermal growth factor receptor binding evidence_type: IEA reference: GO_REF:0000107 note: Donor mouse Ms4a1 IPI cites a study of EGFR interacting with integrin alpha5 and FcepsilonRI (PMID:21349584); the FcepsilonRI beta chain is MS4A2, so the donor annotation looks like a paralog mix-up; REMOVE stands - gene: MTRNR2L10 index: 0 term: id: GO:0005576 label: extracellular region evidence_type: IEA reference: GO_REF:0000044 note: 'Humanin-like nuclear loci (MTRNR2L3/4/7/10/11/13): location and family-node rows removed because no peptide from these loci has been detected (transcript- or homology-level existence only); deliberate microprotein-project decisions; REMOVE stands' - gene: MYH7 index: 4 term: id: GO:0001725 label: stress fiber evidence_type: IEA reference: GO_REF:0000107 note: Donor Myh7 IDA cites a study of non-muscle myosin regulatory light chains and myosin II stability in mouse cells (PMID:21126233); sarcomeric myosin at stress fibers or Z disc is argued against on biology; REMOVE stands ([4],[33]) - gene: NBN index: 222 term: id: GO:0070534 label: protein K63-linked ubiquitination evidence_type: ISS reference: GO_REF:0000024 note: 'ISS from PELI1 (not a homolog): PELI1 is the E3 that K63-ubiquitinates NBN; substrate, not participant; REMOVE stands; recorded as a source defect' - gene: NEUROG1 index: 48 term: id: GO:1905747 label: negative regulation of saliva secretion evidence_type: IGI reference: PMID:23419067 close_call: true note: IGI rows from a case report of a homozygous microdeletion spanning NEUROG1 and two other genes (full text cached); sialorrhoea is secondary to dysphagia, and the Drosophila body-plan term is inapplicable; REMOVE stands ([48],[56]) - gene: NPY5R index: 6 term: id: GO:0003151 label: outflow tract morphogenesis evidence_type: IMP reference: PMID:19593212 close_call: true note: IMP rows to heart morphogenesis terms from a genetic association study of adult left ventricular hypertrophy traits (full text cached); association with an adult trait is not developmental morphogenesis; REMOVE stands ([6],[7]) - gene: NUP98 index: 163 term: id: GO:0042277 label: peptide binding evidence_type: IEA reference: GO_REF:0000107 note: Donor rat Nup98 IDA 'peptide binding' cites the study of the Nup98 peptide-repeat domain as a docking site (PMID:7736573); term mis-describes docking of transport complexes; REMOVE stands - gene: PDGFB index: 144 term: id: GO:0016176 label: superoxide-generating NADPH oxidase activator activity evidence_type: IDA reference: PMID:17942966 close_call: true note: IDA NADPH oxidase activator activity on the secreted ligand (abstract-only); a ligand that triggers ROS production through its receptor is not a direct oxidase activator; REMOVE stands - gene: PEX11B index: 37 term: id: GO:0007165 label: signal transduction evidence_type: ISS reference: GO_REF:0000024 note: ISS signal transduction from PEX11A; the source paper's title states that PEX11beta acts in the absence of extracellular stimuli, a target-specific contradiction; REMOVE stands - gene: PEX16 index: 7 term: id: GO:0005829 label: cytosol evidence_type: TAS reference: Reactome:R-HSA-9603775 note: Three Reactome cytosol rows removed on direct evidence that PEX16 is cotranslationally inserted into the ER with no soluble pool; REMOVE stands - gene: PIK3C3 index: 21 term: id: GO:0043491 label: phosphatidylinositol 3-kinase/protein kinase B signal transduction evidence_type: IEA reference: GO_REF:0000107 note: Donor Pik3c3 IMP cites an inhibitor-based study of PI3K in LTB4-induced enzyme release (PMID:12244116); class III VPS34 is not the class I PI3K of the PI3K/AKT pathway; REMOVE stands - gene: PIKFYVE index: 69 term: id: GO:0080025 label: phosphatidylinositol-3,5-bisphosphate binding evidence_type: ISS reference: GO_REF:0000024 note: ISS rows from STING1 (not a homolog); PIKfyve makes PI(3,5)P2, STING1 binds it; REMOVE stands ([30] already carries a source defect); recorded as a source defect - gene: PNPT1 index: 48 term: id: GO:0005789 label: endoplasmic reticulum membrane evidence_type: IEA reference: GO_REF:0000107 close_call: true note: ER membrane and ribosome transferred from rat Pnpt1 IDA rows citing a 1977 fractionation study (PMID:191106); PNPase is an imported mitochondrial enzyme; REMOVE stands ([48],[51]) - gene: PRG2 index: 13 term: id: GO:0030021 label: extracellular matrix structural constituent conferring compression resistance evidence_type: HDA reference: PMID:28344315 note: Matrisome-derived molecular function (proteoglycan class) on eosinophil major basic protein, which is a proteoglycan in name only; REMOVE stands for the structural-constituent rows of PRG2 and PRG3; the located_in ECM rows are re-actioned - gene: PRG3 index: 10 term: id: GO:0001694 label: histamine biosynthetic process evidence_type: IDA reference: PMID:10318872 note: 'IDA rows to histamine and leukotriene biosynthesis and superoxide generation: MBP2 is the stimulus that triggers release from basophils and neutrophils, not a participant; captured by basophil/neutrophil activation rows; REMOVE stands ([10],[12],[15])' - gene: PRRT1 index: 9 term: id: GO:0030672 label: synaptic vesicle membrane evidence_type: IEA reference: GO_REF:0000107 close_call: true note: Synaptic vesicle membrane transferred from rat Prrt1 IDA citing the SynDIG4 knockout study (PMID:29490264); PRRT1 is a postsynaptic AMPAR auxiliary factor; REMOVE stands - gene: PTPN6 index: 130 term: id: GO:0018108 label: peptidyl-tyrosine phosphorylation evidence_type: IDA reference: PMID:9285411 note: Two IDA rows annotate the phosphatase SHP-1 to peptidyl-tyrosine phosphorylation (abstract-only papers on inhibitory receptors); direction is opposite to the enzyme's activity; REMOVE stands - gene: RAD21 index: 134 term: id: GO:0045841 label: negative regulation of mitotic metaphase/anaphase transition evidence_type: IEA reference: GO_REF:0000107 note: Donor Rad21 IMP on metaphase/anaphase transition; RAD21 is the kleisin cleaved at anaphase onset, a substrate rather than a regulator of the transition; REMOVE stands - gene: RDH11 index: 8 term: id: GO:0033721 label: aldehyde dehydrogenase (NADP+) activity evidence_type: IEA reference: GO_REF:0000107 note: Donor mouse Rdh11 IDA uses the aldehyde dehydrogenase (acid-forming) term for an aldehyde reductase; wrong reaction direction; reductase activity is captured by retinol dehydrogenase (NADP+) rows; REMOVE stands - gene: RPL18A index: 19 term: id: GO:0006941 label: striated muscle contraction evidence_type: NAS reference: PMID:34081545 note: NAS rows cite RPL3L studies and do not concern RPL18A; REMOVE stands ([19],[23]); recorded as a source defect - gene: SCN1A index: 36 term: id: GO:0005654 label: nucleoplasm evidence_type: IDA reference: GO_REF:0000052 close_call: true note: HPA nucleoplasm and nuclear body rows on a 24-transmembrane-segment plasma-membrane channel; topological contradiction; REMOVE stands ([36],[38]) - gene: SCP2 index: 51 term: id: GO:0005102 label: signaling receptor binding evidence_type: IPI reference: PMID:21375735 note: IPI signaling receptor binding with PEX5, the peroxisomal import receptor, which is not a signalling receptor; interaction real, term wrong; REMOVE stands; recorded as a source defect - gene: SIRT1 index: 307 term: id: GO:0042326 label: negative regulation of phosphorylation evidence_type: IMP reference: PMID:17612497 note: 'IMP negative regulation of phosphorylation: abstract states SIRT1 keeps NBS1 hypoacetylated, which is required for its phosphorylation, i.e. the opposite sign; REMOVE stands (also [339] acetylation vs deacetylation)' - gene: SIRT2 index: 82 term: id: GO:0005730 label: nucleolus evidence_type: IDA reference: GO_REF:0000052 close_call: true note: HPA nucleolus removed on the stated ground that published data show SIRT2 excluded from nucleoli when nuclear; REMOVE stands as a positive contradiction - gene: SLC14A1 index: 7 term: id: GO:0005372 label: water transmembrane transporter activity evidence_type: IEA reference: GO_REF:0000107 close_call: true note: Water transport by UT-B is contested (overexpression artefact per PMID:10514515 versus erythrocyte data from knockout mice); removal follows the reviewer's reading that it is not physiological; REMOVE stands ([1],[7]) - gene: SLC25A26 index: 4 term: id: GO:0015860 label: purine nucleoside transmembrane transport evidence_type: IEA reference: GO_REF:0000108 close_call: true note: Purine nucleoside and L-alpha-amino acid transport inferred through GO inter-ontology links from SAM:SAH antiporter activity; removal argues the links are artefacts of SAM's structure (ontology issue, as for FUT8); REMOVE stands ([4],[5]) - gene: SLC26A6 index: 21 term: id: GO:0015797 label: mannitol transmembrane transport evidence_type: ISS reference: GO_REF:0000024 note: Donor paper used [3H]mannitol as a marker of the paracellular pathway (abstract explicit), not as an SLC26A6 substrate; REMOVE stands - gene: SMIM45 index: 0 term: id: GO:0005634 label: nucleus evidence_type: IDA reference: PMID:36593289 note: Experimental rows belong to the 107-residue downstream ORF that the accession represented before its sequence was replaced; removal records a gene-product mismatch documented in the review; REMOVE stands for all SMIM45 rows - gene: SNRPGP15 index: 0 term: id: GO:0000398 label: mRNA splicing, via spliceosome evidence_type: IBA reference: GO_REF:0000033 note: Processed pseudogene with an in-frame stop; all family-derived rows removed; REMOVE stands - gene: SREBF1 index: 19 term: id: GO:0004879 label: nuclear receptor activity evidence_type: IDA reference: PMID:23610160 note: IDA nuclear receptor activity on a bHLH-ZIP factor; wrong protein class whatever the assay; REMOVE stands - gene: SYN2 index: 14 term: id: GO:0031201 label: SNARE complex evidence_type: IEA reference: GO_REF:0000107 note: Donor Syn2 IDA cites a pancreatitis study of the SNARE complex of syntaxin-4, SNAP-23 and VAMP8 (PMID:18535671); looks like a syntaxin/synapsin symbol mix-up; synapsin-2 is not a SNARE; REMOVE stands - gene: SYP index: 9 term: id: GO:0010807 label: regulation of synaptic vesicle priming evidence_type: IEA reference: GO_REF:0000107 close_call: true note: Donor Syp IDA/IMP from the synaptophysin/synaptogyrin quadruple-knockout study; removal argues the family acts after priming; REMOVE stands - gene: SYVN1 index: 24 term: id: GO:0005654 label: nucleoplasm evidence_type: IDA reference: GO_REF:0000052 close_call: true note: HPA nucleoplasm on a six-transmembrane ER membrane protein; topological contradiction; REMOVE stands - gene: TERF2 index: 24 term: id: GO:0003720 label: telomerase activity evidence_type: IDA reference: PMID:23685356 close_call: true note: IDA contributes_to telomerase activity from co-precipitation of TRAP activity with TRF2 (full text read); association, not membership of the telomerase holoenzyme; REMOVE stands ([23],[24],[133]) - gene: TFAP2B index: 0 term: id: GO:0000122 label: negative regulation of transcription by RNA polymerase II evidence_type: IDA reference: PMID:7559606 close_call: true note: IDA negative regulation of transcription from PMID:7559606, where 'AP-2B' is a dominant-negative AP-2alpha splice isoform (stated in the cached abstract); REMOVE stands; recorded as a source defect - gene: TFRC index: 130 term: id: GO:0071466 label: cellular response to xenobiotic stimulus evidence_type: IDA reference: PMID:16254249 close_call: true note: IDA (acts_upstream_of_or_within) response to xenobiotic stimulus from a prion-protein endocytosis study in which TfR1 was an endocytic marker (abstract-only); REMOVE stands - gene: TGFBR3 index: 53 term: id: GO:0006955 label: immune response evidence_type: IMP reference: PMID:16886151 close_call: true note: IMP immune response from a SNP association study of bacteraemia risk in sickle cell anaemia; association, not participation; REMOVE stands - gene: TGOLN2 index: 2 term: id: GO:0005788 label: endoplasmic reticulum lumen evidence_type: TAS reference: Reactome:R-HSA-8952289 note: ER lumen from the Reactome FAM20C substrate reaction on an integral membrane protein of the trans-Golgi network; wrong compartment for a membrane protein and no ER retention; REMOVE stands - gene: TLR4 index: 268 term: id: GO:1903974 label: positive regulation of cellular response to macrophage colony-stimulating factor stimulus evidence_type: IDA reference: PMID:11672593 close_call: true note: IDA positive regulation of cellular response to M-CSF; the paper's title states that TLR2 and TLR4 surface expression is modulated by M-CSF, i.e. TLR4 is the target; REMOVE stands - gene: TOMM20 index: 15 term: id: GO:0071944 label: cell periphery evidence_type: IEA reference: GO_REF:0000107 note: Donor Tomm20 IDA 'cell periphery' cites a study of lysosomal storage in MPS IIIB mouse neurons (PMID:17185018); mitochondrial outer membrane receptor; REMOVE stands - gene: TOMM40 index: 20 term: id: GO:0005743 label: mitochondrial inner membrane evidence_type: IDA reference: PMID:24746669 close_call: true note: IDA mitochondrial inner membrane from the cyclin B1/Cdk1 mitochondrial respiration study (abstract-only); TOMM40 is the outer membrane beta-barrel channel, so the sub-compartment is contradicted by structure; REMOVE stands - gene: TTC21B index: 0 term: id: GO:0003682 label: chromatin binding evidence_type: IEA reference: GO_REF:0000107 note: Donor Ttc21b IDA 'chromatin binding' cites a study of the Alien/ESET complex in E2F1 repression (PMID:22079090), which does not concern the IFT-A subunit; REMOVE stands - gene: TTK index: 24 term: id: GO:0008284 label: positive regulation of cell population proliferation evidence_type: TAS reference: PMID:1639825 close_call: true note: TAS positive regulation of proliferation from the cloning paper's correlation of TTK expression with proliferation; REMOVE stands - gene: TYRP1 index: 3 term: id: GO:0004503 label: tyrosinase activity evidence_type: IDA reference: PMID:21291857 close_call: true note: IDA tyrosinase activity from a study measuring total cellular tyrosinase activity (full text read); purified TYRP1 lacks the activity; REMOVE stands ([2],[3]) - gene: UQCRC1 index: 0 term: id: GO:0017087 label: mitochondrial processing peptidase complex evidence_type: IBA reference: GO_REF:0000033 note: IBA to mitochondrial processing peptidase complex and metal ion binding on the non-catalytic core subunit of complex III; removal argues target-specific loss; REMOVE stands - gene: YAP1 index: 1 term: id: GO:0000976 label: transcription cis-regulatory region binding evidence_type: IDA reference: PMID:18280240 close_call: true note: IDA cis-regulatory region binding from the c-Abl/p73 coactivation paper (abstract only). Removal rests on an independent, quoted contradiction (YAP lacks a DNA-binding domain) and names the kept coactivator terms; contradicted function, REMOVE stands. [2] is the electronic counterpart