description: ComplexPortal-assigned GOA subunit rows that the existing gene review rejected (MARK_AS_OVER_ANNOTATED, MODIFY or REMOVE). Generated by scripts/cp_review_join.py; review_summary is copied from the gene review. count: 502 rows: - organism: DROME gene: cpa qualifier: involved_in term: id: GO:0030989 label: dynein-driven meiotic oscillatory nuclear movement evidence: NAS reference: PMID:22726940 review_action: REMOVE review_summary: Dynein-driven meiotic oscillatory nuclear movement. review_file: genes/DROME/cpa/cpa-ai-review.yaml - organism: DROME gene: cpb qualifier: involved_in term: id: GO:0030989 label: dynein-driven meiotic oscillatory nuclear movement evidence: NAS reference: PMID:22726940 review_action: REMOVE review_summary: Dynein-driven meiotic oscillatory nuclear movement. review_file: genes/DROME/cpb/cpb-ai-review.yaml - organism: ECOLI gene: pstS qualifier: located_in term: id: GO:0016020 label: membrane evidence: NAS reference: PMID:3881386 review_action: REMOVE review_summary: PstS is a periplasmic binding protein, not an integral membrane protein. review_file: genes/ECOLI/pstS/pstS-ai-review.yaml - organism: SCHPO gene: gaa1 qualifier: located_in term: id: GO:0005789 label: endoplasmic reticulum membrane evidence: NAS reference: PMID:15003443 review_action: REMOVE review_summary: Duplicate of the IEA annotation for the same term. Accept one, remove this duplicate. review_file: genes/SCHPO/gaa1/gaa1-ai-review.yaml - organism: SCHPO gene: gaa1 qualifier: involved_in term: id: GO:0016255 label: attachment of GPI anchor to protein evidence: NAS reference: PMID:15003443 review_action: REMOVE review_summary: Duplicate of the IBA annotation for the same term. Accept one, remove this duplicate. review_file: genes/SCHPO/gaa1/gaa1-ai-review.yaml - organism: SCHPO gene: gaa1 qualifier: part_of term: id: GO:0042765 label: GPI-anchor transamidase complex evidence: NAS reference: PMID:15003443 review_action: REMOVE review_summary: Duplicate of the IBA annotation for the same term. Accept one, remove this duplicate. review_file: genes/SCHPO/gaa1/gaa1-ai-review.yaml - organism: human gene: ASCC1 qualifier: involved_in term: id: GO:0006260 label: DNA replication evidence: NAS reference: PMID:29997253 review_action: REMOVE review_summary: The ASCC1/ASCC literature supports alkylation-damage signaling and repair, not a direct ASCC1 role in DNA replication. review_file: genes/human/ASCC1/ASCC1-ai-review.yaml - organism: human gene: ASCC2 qualifier: involved_in term: id: GO:0006260 label: DNA replication evidence: NAS reference: PMID:29997253 review_action: REMOVE review_summary: ASCC2 is involved in DNA alkylation repair, but the specific evidence does not support annotating ASCC2 to DNA replication. review_file: genes/human/ASCC2/ASCC2-ai-review.yaml - organism: human gene: ASCC3 qualifier: involved_in term: id: GO:0006260 label: DNA replication evidence: NAS reference: PMID:29997253 review_action: REMOVE review_summary: The cited ASCC damage-response evidence does not support a general DNA replication role for ASCC3. review_file: genes/human/ASCC3/ASCC3-ai-review.yaml - organism: human gene: BAK1 qualifier: involved_in term: id: GO:0090201 label: negative regulation of release of cytochrome c from mitochondria evidence: IDA reference: PMID:15901672 review_action: REMOVE review_summary: BAK is the restrained target, not the negative regulator, in this anti-apoptotic complex. review_file: genes/human/BAK1/BAK1-ai-review.yaml - organism: human gene: BAK1 qualifier: involved_in term: id: GO:1901029 label: negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway evidence: IDA reference: PMID:15901672 review_action: REMOVE review_summary: BAK is the restrained target, not the inhibitor, of MOMP in this complex. review_file: genes/human/BAK1/BAK1-ai-review.yaml - organism: human gene: CD4 qualifier: involved_in term: id: GO:0030595 label: leukocyte chemotaxis evidence: NAS reference: PMID:27231345 review_action: REMOVE review_summary: NAS for leukocyte chemotaxis, attached to a structural study of an anti-IL-16 therapeutic antibody. review_file: genes/human/CD4/CD4-ai-review.yaml - organism: human gene: CD4 qualifier: involved_in term: id: GO:0050729 label: positive regulation of inflammatory response evidence: NAS reference: PMID:9422780 review_action: REMOVE review_summary: NAS for positive regulation of inflammatory response, cited to the demonstration that caspase-3 processes pro-IL-16 into the bioactive cytokine. review_file: genes/human/CD4/CD4-ai-review.yaml - organism: human gene: CLCN7 qualifier: involved_in term: id: GO:0030321 label: transepithelial chloride transport evidence: IDA reference: PMID:32851177 review_action: REMOVE review_summary: ClC-7 is an intracellular endolysosomal antiporter, not a plasma-membrane mediator of transepithelial chloride flux. This ComplexPortal-derived term mislabels the biological process. review_file: genes/human/CLCN7/CLCN7-ai-review.yaml - organism: human gene: COL4A1 qualifier: involved_in term: id: GO:0030199 label: collagen fibril organization evidence: NAS reference: PMID:29853175 review_action: REMOVE review_summary: Non-traceable author statement from a review of collagen fibril assembly. review_file: genes/human/COL4A1/COL4A1-ai-review.yaml - organism: human gene: DFFB qualifier: involved_in term: id: GO:1902511 label: negative regulation of apoptotic DNA fragmentation evidence: IDA reference: PMID:11371636 review_action: REMOVE review_summary: DFFB is inhibited during negative regulation of DNA fragmentation; it is not the inhibitor. review_file: genes/human/DFFB/DFFB-ai-review.yaml - organism: human gene: DIABLO qualifier: involved_in term: id: GO:0051726 label: regulation of cell cycle evidence: NAS reference: PMID:19153467 review_action: REMOVE review_summary: The cIAP1 structural peptide paper does not establish DIABLO cell-cycle regulation. review_file: genes/human/DIABLO/DIABLO-ai-review.yaml - organism: human gene: DYNC2H1 qualifier: located_in term: id: GO:0001673 label: male germ cell nucleus evidence: NAS reference: PMID:36973253 review_action: REMOVE review_summary: Male germ cell nucleus (NAS) from a study of dynein-1 complexes defined by DYNLRB1/DYNLRB2 in mitotic and male meiotic spindles. The cached full text does not mention DYNC2H1 or dynein-2; dynein in meiotic prophase acts on the cytoplasmic side of the nuclear envelope. review_file: genes/human/DYNC2H1/DYNC2H1-ai-review.yaml - organism: human gene: DYNC2I1 qualifier: located_in term: id: GO:0001673 label: male germ cell nucleus evidence: NAS reference: PMID:36973253 review_action: REMOVE review_summary: Male germ cell nucleus, NAS citing a DYNLRB1/DYNLRB2 dynein-1 study. review_file: genes/human/DYNC2I1/DYNC2I1-ai-review.yaml - organism: human gene: DYNC2I2 qualifier: located_in term: id: GO:0001673 label: male germ cell nucleus evidence: NAS reference: PMID:36973253 review_action: REMOVE review_summary: Male germ cell nucleus, NAS citing a DYNLRB1/DYNLRB2 dynein-1 study. review_file: genes/human/DYNC2I2/DYNC2I2-ai-review.yaml - organism: human gene: DYNC2LI1 qualifier: located_in term: id: GO:0001673 label: male germ cell nucleus evidence: NAS reference: PMID:36973253 review_action: REMOVE review_summary: NAS annotation to male germ cell nucleus, citing a study of DYNLRB1/DYNLRB2-defined dynein-1 complexes. review_file: genes/human/DYNC2LI1/DYNC2LI1-ai-review.yaml - organism: human gene: ESPL1 qualifier: involved_in term: id: GO:0034088 label: maintenance of mitotic sister chromatid cohesion evidence: NAS reference: PMID:34290405 review_action: REMOVE review_summary: The structural paper shows how securin and CDK1-cyclin B1 keep separase inactive before anaphase; maintaining cohesion is the work of cohesin, shugoshin-PP2A and the separase inhibitors, not of separase. review_file: genes/human/ESPL1/ESPL1-ai-review.yaml - organism: human gene: ESPL1 qualifier: involved_in term: id: GO:0034090 label: maintenance of meiotic sister chromatid cohesion evidence: NAS reference: PMID:34290405 review_action: REMOVE review_summary: Meiotic counterpart of the preceding row; the cited cryo-EM study contains no meiotic experiments. review_file: genes/human/ESPL1/ESPL1-ai-review.yaml - organism: human gene: MBL2 qualifier: involved_in term: id: GO:0006508 label: proteolysis evidence: IDA reference: PMID:22691502 review_action: REMOVE review_summary: The proteolysis (C4/C2 cleavage) is carried out by the MASP serine proteases, not by MBL itself - MBL has no protease activity. Annotating MBL with proteolysis attributes an activity of its associated MASP serine proteases to MBL; this is closer to a wrong-gene attribution than an over-annotation. MBL membership in the proteolytic complex is already captured by GO:1905370 (serine-type endopeptidase complex) and its role by the lectin-pathway process annotations. review_file: genes/human/MBL2/MBL2-ai-review.yaml - organism: human gene: PDGFA qualifier: involved_in term: id: GO:0038083 label: peptidyl-tyrosine autophosphorylation evidence: NAS reference: PMID:11297552 review_action: REMOVE review_summary: Peptidyl-tyrosine autophosphorylation is receptor biology, not a process carried out by PDGFA. review_file: genes/human/PDGFA/PDGFA-ai-review.yaml - organism: human gene: PPP3CA qualifier: involved_in term: id: GO:1905665 label: positive regulation of calcium ion import across plasma membrane evidence: NAS reference: PMID:17640527 review_action: REMOVE review_summary: AKAP79/150-anchored calcineurin dominantly suppresses PKA enhancement of L-type CaV1.2 current; the paper does not support calcineurin positively regulating Ca2+ import. review_file: genes/human/PPP3CA/PPP3CA-ai-review.yaml - organism: human gene: PPP3R1 qualifier: involved_in term: id: GO:1905665 label: positive regulation of calcium ion import across plasma membrane evidence: NAS reference: PMID:17640527 review_action: REMOVE review_summary: NAS positive regulation of calcium ion import across plasma membrane from the AKAP79/150-CaV1.2 study. review_file: genes/human/PPP3R1/PPP3R1-ai-review.yaml - organism: human gene: RPL18A qualifier: involved_in term: id: GO:0006941 label: striated muscle contraction evidence: NAS reference: PMID:34081545 review_action: REMOVE review_summary: This annotation appears to be based on a study of RPL3L (muscle-specific ribosomal protein L3-like), not RPL18A directly. The cited paper investigates RPL3L knockdown effects on muscle function. RPL18A may be part of muscle ribosomes but does not have a specific role in muscle contraction distinct from its general ribosomal function. review_file: genes/human/RPL18A/RPL18A-ai-review.yaml - organism: human gene: RPL18A qualifier: involved_in term: id: GO:1901740 label: negative regulation of myoblast fusion evidence: NAS reference: PMID:26684695 review_action: REMOVE review_summary: This annotation appears to be based on a study of RPL3L (muscle-specific ribosomal protein L3-like), not RPL18A. The cited paper title mentions RPL3L affecting myotube growth. This annotation is likely incorrectly associated with RPL18A. review_file: genes/human/RPL18A/RPL18A-ai-review.yaml - organism: human gene: SDHA qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: REMOVE review_summary: NAS annotation from ComplexPortal suggesting SDHA is involved in proton motive force-driven mitochondrial ATP synthesis. This annotation is problematic because Complex II does NOT pump protons across the inner mitochondrial membrane. Unlike Complexes I, III, and IV which translocate protons to generate the proton motive force, Complex II transfers electrons from succinate to ubiquinone without any proton pumping. Complex II contributes to ATP synthesis only indirectly by feeding reduced ubiquinol into the Q pool, which is then oxidized by Complex III (which does pump protons). Annotating SDHA with this term conflates electron donation to the Q pool with proton translocation. review_file: genes/human/SDHA/SDHA-ai-review.yaml - organism: human gene: SDHB qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: REMOVE review_summary: NAS annotation from ComplexPortal suggesting SDHB is involved in proton motive force-driven mitochondrial ATP synthesis. This annotation is problematic because Complex II does NOT pump protons across the inner mitochondrial membrane. Unlike Complexes I, III, and IV which translocate protons to generate the proton motive force, Complex II transfers electrons from succinate to ubiquinone without any proton pumping. Complex II contributes to ATP synthesis only indirectly by feeding reduced ubiquinol into the Q pool, which is then oxidized by Complex III (which does pump protons). review_file: genes/human/SDHB/SDHB-ai-review.yaml - organism: human gene: SDHC qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: REMOVE review_summary: NAS annotation from ComplexPortal suggesting SDHC is involved in proton motive force-driven mitochondrial ATP synthesis. This annotation is problematic because Complex II does NOT pump protons across the inner mitochondrial membrane. Unlike Complexes I, III, and IV which translocate protons to generate the proton motive force, Complex II transfers electrons from succinate to ubiquinone without any proton pumping. Complex II contributes to ATP synthesis only indirectly by feeding reduced ubiquinol into the Q pool, which is then oxidized by Complex III (which does pump protons). The same annotation was marked REMOVE for SDHB in the parallel review. review_file: genes/human/SDHC/SDHC-ai-review.yaml - organism: human gene: SSR2 qualifier: involved_in term: id: GO:0031204 label: post-translational protein targeting to membrane, translocation evidence: NAS reference: PMID:36697828 review_action: REMOVE review_summary: This NAS annotation suggests SSR2/TRAP-beta is involved in post-translational protein translocation. However, the TRAP complex is primarily associated with co-translational translocation, assisting the Sec61 translocon during ribosome- associated protein synthesis and membrane insertion. review_file: genes/human/SSR2/SSR2-ai-review.yaml - organism: human gene: TERT qualifier: involved_in term: id: GO:0000722 label: telomere maintenance via recombination evidence: NAS reference: PMID:20351177 review_action: REMOVE review_summary: This is ALT pathway - TERT functions in telomerase-mediated maintenance, not recombination. review_file: genes/human/TERT/TERT-ai-review.yaml - organism: human gene: TRAF3 qualifier: involved_in term: id: GO:0060337 label: type I interferon-mediated signaling pathway evidence: NAS reference: PMID:25847972 review_action: REMOVE review_summary: Type I interferon-mediated signalling pathway, i.e. signalling downstream of the IFN-alpha/beta receptor. review_file: genes/human/TRAF3/TRAF3-ai-review.yaml - organism: worm gene: ced-3 qualifier: involved_in term: id: GO:1900118 label: negative regulation of execution phase of apoptosis evidence: IMP reference: PMID:10101135 review_action: REMOVE review_summary: Negative regulation of execution is the role of MAC-1/CSP/NPP-14-like inhibitors, not the inhibited CED-3 protease. review_file: genes/worm/ced-3/ced-3-ai-review.yaml - organism: worm gene: ced-4 qualifier: involved_in term: id: GO:1900118 label: negative regulation of execution phase of apoptosis evidence: IMP reference: PMID:10101135 review_action: REMOVE review_summary: MAC-1 is the inhibitor in this pathway; CED-4 is not a negative regulator of apoptotic execution. review_file: genes/worm/ced-4/ced-4-ai-review.yaml - organism: yeast gene: CAC2 qualifier: part_of term: id: GO:0000786 label: nucleosome evidence: IDA reference: PMID:30239791 review_action: REMOVE review_summary: Complex Portal annotation placing CAC2 (a CAF-1 subunit) as part_of the nucleosome, citing a review of CAF-1 mechanism (PMID:30239791). review_file: genes/yeast/CAC2/CAC2-ai-review.yaml - organism: yeast gene: MSI1 qualifier: part_of term: id: GO:0000786 label: nucleosome evidence: IDA reference: PMID:30239791 review_action: REMOVE review_summary: Complex Portal annotation placing MSI1 (a CAF-1 subunit) as part_of the nucleosome, citing a review of CAF-1 mechanism (PMID:30239791). review_file: genes/yeast/MSI1/MSI1-ai-review.yaml - organism: yeast gene: RLF2 qualifier: part_of term: id: GO:0000786 label: nucleosome evidence: IDA reference: PMID:30239791 review_action: REMOVE review_summary: Complex Portal annotation placing RLF2 (a CAF-1 subunit) as part_of the nucleosome, citing a review of CAF-1 mechanism (PMID:30239791). review_file: genes/yeast/RLF2/RLF2-ai-review.yaml - organism: yeast gene: RPD3 qualifier: involved_in term: id: GO:0006334 label: nucleosome assembly evidence: NAS reference: PMID:22177115 review_action: REMOVE review_summary: Mechanistically incorrect; Rpd3 stabilizes chromatin, not assembles nucleosomes review_file: genes/yeast/RPD3/RPD3-ai-review.yaml - organism: yeast gene: RPD3 qualifier: involved_in term: id: GO:0006979 label: response to oxidative stress evidence: NAS reference: PMID:23878396 review_action: REMOVE review_summary: Insufficient direct evidence; paper focuses on Snt2 component, not Rpd3-specific function review_file: genes/yeast/RPD3/RPD3-ai-review.yaml - organism: ARATH gene: CYP71A12 qualifier: involved_in term: id: GO:0006952 label: defense response evidence: NAS reference: PMID:31511315 review_action: MODIFY review_summary: Author statement that camalexin pathway enzymes act in defense. CYP71A12 products (camalexin, ICA derivatives, 4-OH-ICN) are inducible antimicrobial defense metabolites. review_file: genes/ARATH/CYP71A12/CYP71A12-ai-review.yaml - organism: DROME gene: Caf1-55 qualifier: involved_in term: id: GO:0031507 label: heterochromatin formation evidence: NAS reference: PMID:35193659 review_action: MODIFY review_summary: PRC2 membership underlies a role in repressive chromatin formation. review_file: genes/DROME/Caf1-55/Caf1-55-ai-review.yaml - organism: DROME gene: Dph1 qualifier: part_of term: id: GO:1902494 label: catalytic complex evidence: NAS reference: PMID:30877278 review_action: MODIFY review_summary: Catalytic complex is correct but uninformative. review_file: genes/DROME/Dph1/Dph1-ai-review.yaml - organism: DROME gene: Dph2 qualifier: part_of term: id: GO:1902494 label: catalytic complex evidence: NAS reference: PMID:30877278 review_action: MODIFY review_summary: Catalytic complex is correct but uninformative. review_file: genes/DROME/Dph2/Dph2-ai-review.yaml - organism: DROME gene: kirre qualifier: involved_in term: id: GO:1901739 label: regulation of myoblast fusion evidence: NAS reference: PMID:11684662 review_action: MODIFY review_summary: Regulation of myoblast fusion. review_file: genes/DROME/kirre/kirre-ai-review.yaml - organism: DROME gene: kirre qualifier: involved_in term: id: GO:1901739 label: regulation of myoblast fusion evidence: IDA reference: PMID:11684662 review_action: MODIFY review_summary: Regulation of myoblast fusion. review_file: genes/DROME/kirre/kirre-ai-review.yaml - organism: DROME gene: rst qualifier: involved_in term: id: GO:1901739 label: regulation of myoblast fusion evidence: NAS reference: PMID:11684662 review_action: MODIFY review_summary: Regulation of myoblast fusion. review_file: genes/DROME/rst/rst-ai-review.yaml - organism: DROME gene: rst qualifier: involved_in term: id: GO:1901739 label: regulation of myoblast fusion evidence: IDA reference: PMID:11684662 review_action: MODIFY review_summary: Regulation of myoblast fusion. review_file: genes/DROME/rst/rst-ai-review.yaml - organism: DROME gene: sgg qualifier: involved_in term: id: GO:0043161 label: proteasome-mediated ubiquitin-dependent protein catabolic process evidence: NAS reference: PMID:24931405 review_action: MODIFY review_summary: ComplexPortal-derived process for the destruction complex. review_file: genes/DROME/sgg/sgg-ai-review.yaml - organism: ECOLI gene: SecD qualifier: located_in term: id: GO:0016020 label: membrane evidence: NAS reference: PMID:8253068 review_action: MODIFY review_summary: SecD is specifically in the bacterial plasma membrane. review_file: genes/ECOLI/SecD/SecD-ai-review.yaml - organism: ECOLI gene: SecE qualifier: located_in term: id: GO:0016020 label: membrane evidence: IDA reference: PMID:8253068 review_action: MODIFY review_summary: SecE is specifically an inner/plasma membrane protein. review_file: genes/ECOLI/SecE/SecE-ai-review.yaml - organism: ECOLI gene: SecE qualifier: located_in term: id: GO:0016020 label: membrane evidence: NAS reference: PMID:8253068 review_action: MODIFY review_summary: SecE is specifically an inner/plasma membrane protein. review_file: genes/ECOLI/SecE/SecE-ai-review.yaml - organism: ECOLI gene: SecF qualifier: located_in term: id: GO:0016020 label: membrane evidence: NAS reference: PMID:8253068 review_action: MODIFY review_summary: SecF is specifically in the bacterial plasma membrane. review_file: genes/ECOLI/SecF/SecF-ai-review.yaml - organism: ECOLI gene: SecG qualifier: located_in term: id: GO:0016020 label: membrane evidence: IDA reference: PMID:8253068 review_action: MODIFY review_summary: SecG is specifically an inner/plasma membrane protein. review_file: genes/ECOLI/SecG/SecG-ai-review.yaml - organism: ECOLI gene: SecG qualifier: located_in term: id: GO:0016020 label: membrane evidence: NAS reference: PMID:8253068 review_action: MODIFY review_summary: SecG is specifically an inner/plasma membrane protein. review_file: genes/ECOLI/SecG/SecG-ai-review.yaml - organism: ECOLI gene: SecY qualifier: located_in term: id: GO:0016020 label: membrane evidence: IDA reference: PMID:8253068 review_action: MODIFY review_summary: SecY is specifically an inner/plasma membrane protein. review_file: genes/ECOLI/SecY/SecY-ai-review.yaml - organism: ECOLI gene: SecY qualifier: located_in term: id: GO:0016020 label: membrane evidence: NAS reference: PMID:8253068 review_action: MODIFY review_summary: SecY is specifically an inner/plasma membrane protein. review_file: genes/ECOLI/SecY/SecY-ai-review.yaml - organism: ECOLI gene: YajC qualifier: located_in term: id: GO:0016020 label: membrane evidence: NAS reference: PMID:8253068 review_action: MODIFY review_summary: YajC is specifically a plasma-membrane Sec accessory subunit. review_file: genes/ECOLI/YajC/YajC-ai-review.yaml - organism: ECOLI gene: fliI qualifier: located_in term: id: GO:0009288 label: bacterial-type flagellum evidence: NAS reference: PMID:31337100 review_action: MODIFY review_summary: FliI is part of the cytoplasmic ATPase ring complex of the flagellar type III export apparatus at the base of the flagellum. It is not part of the rod, hook or filament. review_file: genes/ECOLI/fliI/fliI-ai-review.yaml - organism: ECOLI gene: lpd qualifier: involved_in term: id: GO:0006730 label: one-carbon metabolic process evidence: NAS reference: PMID:8375392 review_action: MODIFY review_summary: The one-carbon process assertion reflects LpdA's glycine-cleavage role. review_file: genes/ECOLI/lpd/lpd-ai-review.yaml - organism: ECOLI gene: lpd qualifier: involved_in term: id: GO:0042867 label: pyruvate catabolic process evidence: NAS reference: PMID:3903169 review_action: MODIFY review_summary: LpdA participates in pyruvate catabolism as the E3 enzyme of pyruvate dehydrogenase. review_file: genes/ECOLI/lpd/lpd-ai-review.yaml - organism: SCHPO gene: poz1 qualifier: involved_in term: id: GO:0032206 label: positive regulation of telomere maintenance evidence: NAS reference: PMID:18535244 review_action: MODIFY review_summary: This annotation captures that Poz1 affects telomere maintenance, but the direction and specificity are off. Poz1 primarily restrains telomerase-dependent lengthening rather than positively promoting it. review_file: genes/SCHPO/poz1/poz1-ai-review.yaml - organism: SCHPO gene: rfc3 qualifier: involved_in term: id: GO:0006260 label: DNA replication evidence: NAS reference: PMID:20505337 review_action: MODIFY review_summary: DNA replication is reviewed in the context of rfc3. review_file: genes/SCHPO/rfc3/rfc3-ai-review.yaml - organism: human gene: A1CF qualifier: involved_in term: id: GO:0016556 label: mRNA modification evidence: IDA reference: PMID:11134005 review_action: MODIFY review_summary: The cited study concerns C-to-U modification of APOB mRNA. review_file: genes/human/A1CF/A1CF-ai-review.yaml - organism: human gene: A1CF qualifier: part_of term: id: GO:0045293 label: mRNA editing complex evidence: NAS reference: PMID:11134005 review_action: MODIFY review_summary: A1CF belongs specifically to the APOB mRNA editing enzyme complex. review_file: genes/human/A1CF/A1CF-ai-review.yaml - organism: human gene: ABCB10 qualifier: involved_in term: id: GO:0006783 label: heme biosynthetic process evidence: NAS reference: PMID:30765471 review_action: MODIFY review_summary: 'This row is NOT the ALA-export inference the other two GO:0006783 rows rest on, and needs its own argument. It is a ComplexPortal NAS assignment from PMID:30765471, which identified a crosslinking/MS-defined complex of ferrochelatase (FECH), ABCB7 and ABCB10 and titled it "required for heme biosynthesis". That curator was asserting complex-level participation via FECH - the terminal enzyme of the pathway - not that ABCB10 itself transports a heme intermediate, so rebutting ALA transport does not engage this evidence. The term is still wrong for ABCB10, on narrower grounds. An annotation inherited from a partner''s catalytic role is a complex-level attribution, and ABCB10''s own demonstrated contribution to hemoglobinization is regulatory: ATP-hydrolysis-dependent relief of Bach1 repression of the heme transcriptional programme, and stabilisation of mitoferrin-1 for mitochondrial iron import. GO:0070455 positive regulation of heme biosynthetic process, already on this gene by ISS, says that without asserting that ABCB10 carries out a step. The FECH association itself is not lost - it is carried by the complex-membership annotations this review retains, which is where a complex-level fact belongs.' review_file: genes/human/ABCB10/ABCB10-ai-review.yaml - organism: human gene: ABCC8 qualifier: involved_in term: id: GO:1990573 label: potassium ion import across plasma membrane evidence: ISS reference: GO_REF:0000114 review_action: MODIFY review_summary: Direction-independent potassium transport is supported, but this donor does not establish physiological human K+ import. review_file: genes/human/ABCC8/ABCC8-ai-review.yaml - organism: human gene: ABRAXAS1 qualifier: involved_in term: id: GO:0006282 label: regulation of DNA repair evidence: NAS reference: PMID:20656689 review_action: MODIFY review_summary: The broad regulation-of-DNA-repair annotation is directionally correct but less precise than positive regulation of DNA repair for ABRAXAS1. review_file: genes/human/ABRAXAS1/ABRAXAS1-ai-review.yaml - organism: human gene: ABRAXAS1 qualifier: involved_in term: id: GO:0044818 label: mitotic G2/M transition checkpoint evidence: NAS reference: PMID:22369660 review_action: MODIFY review_summary: The ComplexPortal/NAS checkpoint annotation is real but should be represented using the more specific DNA-damage checkpoint signaling term. review_file: genes/human/ABRAXAS1/ABRAXAS1-ai-review.yaml - organism: human gene: ABRAXAS2 qualifier: involved_in term: id: GO:0034516 label: response to vitamin B6 evidence: NAS reference: PMID:31142841 review_action: MODIFY review_summary: Vitamin B6/PLP regulates SHMT2 oligomer state and thus BRISC-SHMT2 assembly, but ABRAXAS2 is not best described as executing a vitamin B6 response. review_file: genes/human/ABRAXAS2/ABRAXAS2-ai-review.yaml - organism: human gene: ACIN1 qualifier: involved_in term: id: GO:0050684 label: regulation of mRNA processing evidence: IDA reference: PMID:12665594 review_action: MODIFY review_summary: Regulation of mRNA processing is sound but can be made more specific. review_file: genes/human/ACIN1/ACIN1-ai-review.yaml - organism: human gene: AHCTF1 qualifier: involved_in term: id: GO:0006913 label: nucleocytoplasmic transport evidence: NAS reference: PMID:27016207 review_action: MODIFY review_summary: Nucleocytoplasmic transport is a real downstream function of assembled NPCs, but it is too broad for AHCTF1 itself. review_file: genes/human/AHCTF1/AHCTF1-ai-review.yaml - organism: human gene: AMH qualifier: involved_in term: id: GO:0007530 label: sex determination evidence: NAS reference: PMID:34155118 review_action: MODIFY review_summary: Sex determination, from the structure paper. Modified to development of primary male sexual characteristics, the specific male-differentiation term the gene already carries. review_file: genes/human/AMH/AMH-ai-review.yaml - organism: human gene: AP3B2 qualifier: involved_in term: id: GO:0035654 label: clathrin-coated vesicle cargo loading, AP-3-mediated evidence: NAS reference: PMID:9545220 review_action: MODIFY review_summary: NAS annotation from ComplexPortal citing the key paper demonstrating AP-3 association with clathrin. AP-3 mediates cargo recognition and vesicle loading, but the clathrin-coated qualifier is too strong for neuronal AP3B2. review_file: genes/human/AP3B2/AP3B2-ai-review.yaml - organism: human gene: AP3D1 qualifier: involved_in term: id: GO:0016183 label: synaptic vesicle coating evidence: NAS reference: PMID:15537701 review_action: MODIFY review_summary: The GO term means clathrin-coated pit formation at the presynaptic plasma membrane. AP-3 does not act there; the cited paper is about endosomal sorting of synaptic-vesicle proteins. review_file: genes/human/AP3D1/AP3D1-ai-review.yaml - organism: human gene: AP3D1 qualifier: involved_in term: id: GO:0035654 label: clathrin-coated vesicle cargo loading, AP-3-mediated evidence: NAS reference: PMID:9545220 review_action: MODIFY review_summary: Cargo loading is right; the clathrin-coated-vesicle framing is not, and the clathrin contact that generated it was beta-3's, not delta's. review_file: genes/human/AP3D1/AP3D1-ai-review.yaml - organism: human gene: AP3M1 qualifier: involved_in term: id: GO:0035654 label: clathrin-coated vesicle cargo loading, AP-3-mediated evidence: NAS reference: PMID:9545220 review_action: MODIFY review_summary: '''Clathrin-coated vesicle cargo loading, AP-3-mediated'', asserted by ComplexPortal and cited to the 1998 Science report that mammalian AP-3 binds clathrin through the beta3 appendage. The AP-3-mediated cargo-loading half of the term is exactly right for this protein - it is what the mu subunit does. The clathrin-coated-vesicle half is the problem, and the term''s own definition already hedges it (''in some organisms, links clathrin'').' review_file: genes/human/AP3M1/AP3M1-ai-review.yaml - organism: human gene: AP3M2 qualifier: involved_in term: id: GO:0016183 label: synaptic vesicle coating evidence: NAS reference: PMID:15537701 review_action: MODIFY review_summary: Synaptic vesicle coating, asserted by ComplexPortal for the neuronal AP-3 complex. The GO term is defined as clathrin-coated-pit formation in the presynaptic endocytic zone, which is the AP-2 pathway, not the AP-3 one. review_file: genes/human/AP3M2/AP3M2-ai-review.yaml - organism: human gene: AP3S1 qualifier: involved_in term: id: GO:0016183 label: synaptic vesicle coating evidence: NAS reference: PMID:15537701 review_action: MODIFY review_summary: Synaptic vesicle coating, from ComplexPortal. AP-3 does coat synaptic vesicles, but this term's definition describes coated-pit formation at the presynaptic plasma membrane, which is AP-2 territory. review_file: genes/human/AP3S1/AP3S1-ai-review.yaml - organism: human gene: AP3S2 qualifier: involved_in term: id: GO:0016183 label: synaptic vesicle coating evidence: NAS reference: PMID:15537701 review_action: MODIFY review_summary: The term means clathrin-coated pit formation at the presynaptic plasma membrane, which is not what AP-3 does and not what the cited paper reports. review_file: genes/human/AP3S2/AP3S2-ai-review.yaml - organism: human gene: AP3S2 qualifier: involved_in term: id: GO:0035654 label: clathrin-coated vesicle cargo loading, AP-3-mediated evidence: NAS reference: PMID:9545220 review_action: MODIFY review_summary: Cargo loading by AP-3 is exactly what sigma-3B contributes to; the clathrin-coated-vesicle half of the term is the part that has since been overturned [PMID:42139345]. review_file: genes/human/AP3S2/AP3S2-ai-review.yaml - organism: human gene: AP4E1 qualifier: located_in term: id: GO:0005802 label: trans-Golgi network evidence: NAS reference: PMID:10436028 review_action: MODIFY review_summary: Refine the broad Golgi/TGN compartment to its membrane-associated AP-4 pool. review_file: genes/human/AP4E1/AP4E1-ai-review.yaml - organism: human gene: AP5B1 qualifier: involved_in term: id: GO:0016192 label: vesicle-mediated transport evidence: NAS reference: PMID:22022230 review_action: MODIFY review_summary: 'Vesicle-mediated transport, asserted by ComplexPortal for CPX-5181. True but the least informative statement that could be made about this gene: GO:0016192 is the grandparent of GO:0016197 endosomal transport, which this gene already carries by IMP, IBA and IEA.' review_file: genes/human/AP5B1/AP5B1-ai-review.yaml - organism: human gene: AP5M1 qualifier: involved_in term: id: GO:0016192 label: vesicle-mediated transport evidence: NAS reference: PMID:22022230 review_action: MODIFY review_summary: True parent, but two levels shallower than what the cited paper establishes, and shallower than the endosomal transport term the same gene already carries. review_file: genes/human/AP5M1/AP5M1-ai-review.yaml - organism: human gene: AP5Z1 qualifier: involved_in term: id: GO:0016192 label: vesicle-mediated transport evidence: NAS reference: PMID:22022230 review_action: MODIFY review_summary: Endosomal transport is more specific than general vesicle-mediated transport. review_file: genes/human/AP5Z1/AP5Z1-ai-review.yaml - organism: human gene: ATF6 qualifier: involved_in term: id: GO:0036503 label: ERAD quality control pathway evidence: NAS reference: PMID:17765680 review_action: MODIFY review_summary: Refine ERAD quality control pathway to positive regulation of ERAD pathway. review_file: genes/human/ATF6/ATF6-ai-review.yaml - organism: human gene: ATG14 qualifier: part_of term: id: GO:0035032 label: phosphatidylinositol 3-kinase complex, class III evidence: IPI reference: PMID:25490155 review_action: MODIFY review_summary: The class III PI3K complex assignment is correct but should be narrowed to the ATG14-containing PI3KC3-C1/type I autophagy complex. review_file: genes/human/ATG14/ATG14-ai-review.yaml - organism: human gene: ATG14 qualifier: part_of term: id: GO:0035032 label: phosphatidylinositol 3-kinase complex, class III evidence: IPI reference: PMID:40442316 review_action: MODIFY review_summary: The class III PI3K complex assignment is correct but should be narrowed to the ATG14-containing PI3KC3-C1/type I autophagy complex. review_file: genes/human/ATG14/ATG14-ai-review.yaml - organism: human gene: ATP6V0A4 qualifier: involved_in term: id: GO:0051452 label: intracellular pH reduction evidence: NAS reference: PMID:32001091 review_action: MODIFY review_summary: Intracellular pH reduction captures the general V-ATPase effect but is less precise than vacuolar acidification and proton transport. review_file: genes/human/ATP6V0A4/ATP6V0A4-ai-review.yaml - organism: human gene: ATP6V1H qualifier: located_in term: id: GO:0016020 label: membrane evidence: IDA reference: PMID:33065002 review_action: MODIFY review_summary: IDA from cryo-EM structure study; this directly shows subunit H as part of the membrane-associated V-ATPase holoenzyme. review_file: genes/human/ATP6V1H/ATP6V1H-ai-review.yaml - organism: human gene: ATRX qualifier: located_in term: id: GO:0016604 label: nuclear body evidence: IPI reference: PMID:12953102 review_action: MODIFY review_summary: The cited ATRX–DAXX study identifies PML nuclear bodies. review_file: genes/human/ATRX/ATRX-ai-review.yaml - organism: human gene: BAG6 qualifier: involved_in term: id: GO:0006511 label: ubiquitin-dependent protein catabolic process evidence: IDA reference: PMID:20676083 review_action: MODIFY review_summary: PMID:20676083 is about ribosome-associated capture and handoff of tail-anchored proteins to TRC40, not a generic ubiquitin-dependent catabolic process. review_file: genes/human/BAG6/BAG6-ai-review.yaml - organism: human gene: BAG6 qualifier: involved_in term: id: GO:0031647 label: regulation of protein stability evidence: IDA reference: PMID:21636303 review_action: MODIFY review_summary: The paper supports holdase/chaperone behavior rather than a broad generic regulation-of-stability process. review_file: genes/human/BAG6/BAG6-ai-review.yaml - organism: human gene: BAK1 qualifier: involved_in term: id: GO:0090200 label: positive regulation of release of cytochrome c from mitochondria evidence: NAS reference: PMID:32929280 review_action: MODIFY review_summary: Positive regulation of cytochrome-c release should be captured as direct cytochrome-c release. review_file: genes/human/BAK1/BAK1-ai-review.yaml - organism: human gene: BCL10 qualifier: involved_in term: id: GO:0043122 label: regulation of canonical NF-kappaB signal transduction evidence: NAS reference: PMID:19118383 review_action: MODIFY review_summary: BCL10 positively regulates the canonical NF-kappaB pathway. review_file: genes/human/BCL10/BCL10-ai-review.yaml - organism: human gene: BCL10 qualifier: involved_in term: id: GO:0043122 label: regulation of canonical NF-kappaB signal transduction evidence: NAS reference: PMID:27071417 review_action: MODIFY review_summary: BCL10 positively regulates the canonical NF-kappaB pathway. review_file: genes/human/BCL10/BCL10-ai-review.yaml - organism: human gene: BCL10 qualifier: involved_in term: id: GO:0043122 label: regulation of canonical NF-kappaB signal transduction evidence: NAS reference: PMID:30467369 review_action: MODIFY review_summary: BCL10 positively regulates the canonical NF-kappaB pathway. review_file: genes/human/BCL10/BCL10-ai-review.yaml - organism: human gene: BCL2L11 qualifier: involved_in term: id: GO:0042981 label: regulation of apoptotic process evidence: IDA reference: PMID:18209102 review_action: MODIFY review_summary: The apoptosis-regulation row is correct but too broad for BIM. review_file: genes/human/BCL2L11/BCL2L11-ai-review.yaml - organism: human gene: CCDC47 qualifier: involved_in term: id: GO:0045048 label: protein insertion into ER membrane evidence: IDA reference: PMID:32814900 review_action: MODIFY review_summary: CCDC47 promotes biogenesis of multi-spanning membrane proteins as part of the PAT complex; the more specific multi-pass insertion term better captures this. review_file: genes/human/CCDC47/CCDC47-ai-review.yaml - organism: human gene: CDC20 qualifier: involved_in term: id: GO:0007346 label: regulation of mitotic cell cycle evidence: NAS reference: PMID:15678131 review_action: MODIFY review_summary: Review of APC/C structure, regulation and substrate recognition; CDC20 as the mitotic coactivator. review_file: genes/human/CDC20/CDC20-ai-review.yaml - organism: human gene: CDC20 qualifier: involved_in term: id: GO:0051445 label: regulation of meiotic cell cycle evidence: NAS reference: PMID:15678131 review_action: MODIFY review_summary: Review noting APC/C roles in meiosis. review_file: genes/human/CDC20/CDC20-ai-review.yaml - organism: human gene: CFH qualifier: involved_in term: id: GO:0030451 label: regulation of complement activation, alternative pathway evidence: IDA reference: PMID:20378178 review_action: MODIFY review_summary: C-terminal C3b/C3d recognition supports inhibitory alternative-pathway control. review_file: genes/human/CFH/CFH-ai-review.yaml - organism: human gene: CFH qualifier: involved_in term: id: GO:0030451 label: regulation of complement activation, alternative pathway evidence: IDA reference: PMID:28671664 review_action: MODIFY review_summary: Factor-H-dependent C3b processing negatively regulates pathway amplification. review_file: genes/human/CFH/CFH-ai-review.yaml - organism: human gene: CHMP1B qualifier: involved_in term: id: GO:0051469 label: vesicle fusion with vacuole evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: Yeast-centric terminology for MVB-lysosome fusion. review_file: genes/human/CHMP1B/CHMP1B-ai-review.yaml - organism: human gene: CHMP2B qualifier: part_of term: id: GO:0005643 label: nuclear pore evidence: IDA reference: PMID:26040713 review_action: MODIFY review_summary: Refine the location to the nuclear envelope. review_file: genes/human/CHMP2B/CHMP2B-ai-review.yaml - organism: human gene: CHMP4A qualifier: involved_in term: id: GO:0051469 label: vesicle fusion with vacuole evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: vesicle fusion with vacuole overstates a direct vesicle-fusion role for CHMP4A. review_file: genes/human/CHMP4A/CHMP4A-ai-review.yaml - organism: human gene: CHMP4A qualifier: involved_in term: id: GO:0061763 label: multivesicular body-lysosome fusion evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: multivesicular body-lysosome fusion overstates a direct vesicle-fusion role for CHMP4A. review_file: genes/human/CHMP4A/CHMP4A-ai-review.yaml - organism: human gene: CHMP4B qualifier: involved_in term: id: GO:0051469 label: vesicle fusion with vacuole evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: 'CHMP4B annotation should be replaced with a more accurate ESCRT-III term: vesicle fusion with vacuole.' review_file: genes/human/CHMP4B/CHMP4B-ai-review.yaml - organism: human gene: CHMP4B qualifier: involved_in term: id: GO:0061763 label: multivesicular body-lysosome fusion evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: 'CHMP4B annotation should be replaced with a more accurate ESCRT-III term: multivesicular body-lysosome fusion.' review_file: genes/human/CHMP4B/CHMP4B-ai-review.yaml - organism: human gene: CHMP4C qualifier: involved_in term: id: GO:0051469 label: vesicle fusion with vacuole evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: 'CHMP4C annotation should be replaced with a less over-specific ESCRT/MVB term: vesicle fusion with vacuole.' review_file: genes/human/CHMP4C/CHMP4C-ai-review.yaml - organism: human gene: CHMP4C qualifier: involved_in term: id: GO:0061763 label: multivesicular body-lysosome fusion evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: 'CHMP4C annotation should be replaced with a less over-specific ESCRT/MVB term: multivesicular body-lysosome fusion.' review_file: genes/human/CHMP4C/CHMP4C-ai-review.yaml - organism: human gene: CHMP5 qualifier: involved_in term: id: GO:0051469 label: vesicle fusion with vacuole evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: vesicle fusion with vacuole is an over-specific/organellar endpoint for CHMP5 and should be generalized to late endosome-to-lysosome transport. review_file: genes/human/CHMP5/CHMP5-ai-review.yaml - organism: human gene: CHMP5 qualifier: involved_in term: id: GO:0061763 label: multivesicular body-lysosome fusion evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: multivesicular body-lysosome fusion is an over-specific/organellar endpoint for CHMP5 and should be generalized to late endosome-to-lysosome transport. review_file: genes/human/CHMP5/CHMP5-ai-review.yaml - organism: human gene: CHMP6 qualifier: involved_in term: id: GO:0051469 label: vesicle fusion with vacuole evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: 'This transport/fusion annotation should be replaced with the better-supported CHMP6 endolysosomal cargo-sorting route: vesicle fusion with vacuole.' review_file: genes/human/CHMP6/CHMP6-ai-review.yaml - organism: human gene: CHMP6 qualifier: involved_in term: id: GO:0061763 label: multivesicular body-lysosome fusion evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: 'This transport/fusion annotation should be replaced with the better-supported CHMP6 endolysosomal cargo-sorting route: multivesicular body-lysosome fusion.' review_file: genes/human/CHMP6/CHMP6-ai-review.yaml - organism: human gene: CHMP7 qualifier: part_of term: id: GO:0005643 label: nuclear pore evidence: IDA reference: PMID:26040713 review_action: MODIFY review_summary: The localization essence is nuclear-envelope recruitment, not stable membership in nuclear pore. review_file: genes/human/CHMP7/CHMP7-ai-review.yaml - organism: human gene: CHMP7 qualifier: involved_in term: id: GO:0051469 label: vesicle fusion with vacuole evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: 'This fusion/vacuole annotation should be generalized to the better-supported endolysosomal route: vesicle fusion with vacuole.' review_file: genes/human/CHMP7/CHMP7-ai-review.yaml - organism: human gene: CHMP7 qualifier: involved_in term: id: GO:0061763 label: multivesicular body-lysosome fusion evidence: NAS reference: PMID:16505166 review_action: MODIFY review_summary: 'This fusion/vacuole annotation should be generalized to the better-supported endolysosomal route: multivesicular body-lysosome fusion.' review_file: genes/human/CHMP7/CHMP7-ai-review.yaml - organism: human gene: CHMP7 qualifier: involved_in term: id: GO:1901673 label: regulation of mitotic spindle assembly evidence: IMP reference: PMID:20616062 review_action: MODIFY review_summary: 'The cell-cycle/spindle wording is too broad for CHMP7: regulation of mitotic spindle assembly.' review_file: genes/human/CHMP7/CHMP7-ai-review.yaml - organism: human gene: CLPP qualifier: part_of term: id: GO:0009368 label: endopeptidase Clp complex evidence: IPI reference: PMID:15522782 review_action: MODIFY review_summary: Structural study of human mitochondrial CLPP as the proteolytic component of ClpXP. review_file: genes/human/CLPP/CLPP-ai-review.yaml - organism: human gene: COPS2 qualifier: involved_in term: id: GO:0045116 label: protein neddylation evidence: NAS reference: PMID:24421388 review_action: MODIFY review_summary: The CSN complex primarily performs deneddylation (removal of NEDD8), not neddylation (addition of NEDD8). This annotation appears to be an error or misunderstanding of CSN function. review_file: genes/human/COPS2/COPS2-ai-review.yaml - organism: human gene: COPS8 qualifier: involved_in term: id: GO:0045116 label: protein neddylation evidence: NAS reference: PMID:24421388 review_action: MODIFY review_summary: This annotation is problematic. The CSN complex is involved in protein DENEDDYLATION (removal of NEDD8), not neddylation (attachment of NEDD8). PMID:24421388 discusses CSN regulation of neddylation/deneddylation cycles but CSN is a deneddylase, not a neddylation enzyme. review_file: genes/human/COPS8/COPS8-ai-review.yaml - organism: human gene: COX5B qualifier: located_in term: id: GO:0031966 label: mitochondrial membrane evidence: IDA reference: PMID:30030519 review_action: MODIFY review_summary: Broad term for mitochondrial membranes (includes both inner and outer). COX5B specifically on inner membrane. review_file: genes/human/COX5B/COX5B-ai-review.yaml - organism: human gene: CUL1 qualifier: involved_in term: id: GO:0051298 label: centrosome duplication evidence: NAS reference: PMID:34388369 review_action: MODIFY review_summary: SCF(FBXW5) degrades SAS-6 and SCF(cyclin F) degrades CP110 to restrain centrosome duplication; the cited reference, however, is the signal peptidase complex structure. review_file: genes/human/CUL1/CUL1-ai-review.yaml - organism: human gene: CUL1 qualifier: involved_in term: id: GO:0060271 label: cilium assembly evidence: NAS reference: PMID:34368969 review_action: MODIFY review_summary: SCF(Fbxw5) degrades the kinesin-13 MCAK in G2, permitting ciliogenesis in the next G1/G0. review_file: genes/human/CUL1/CUL1-ai-review.yaml - organism: human gene: DIABLO qualifier: involved_in term: id: GO:0042981 label: regulation of apoptotic process evidence: NAS reference: PMID:19153467 review_action: MODIFY review_summary: DIABLO promotes intrinsic apoptotic signaling by neutralizing IAPs. review_file: genes/human/DIABLO/DIABLO-ai-review.yaml - organism: human gene: DPM3 qualifier: involved_in term: id: GO:0043048 label: dolichyl monophosphate biosynthetic process evidence: IDA reference: PMID:10835346 review_action: MODIFY review_summary: IDA annotation to dolichyl monophosphate (Dol-P) biosynthesis. This term denotes formation of dolichyl monophosphate, which is the SUBSTRATE of DPM synthase, not its product. DPM synthase (and thus DPM3) makes Dol-P-Man from Dol-P + GDP-mannose; it does not synthesize Dol-P itself. The evidence in PMID:10835346 concerns restoration of Dol-P-Man (DPM) biosynthesis. review_file: genes/human/DPM3/DPM3-ai-review.yaml - organism: human gene: DYNC1H1 qualifier: involved_in term: id: GO:0032388 label: positive regulation of intracellular transport evidence: NAS reference: PMID:33957056 review_action: MODIFY review_summary: Positive regulation of intracellular transport (NAS) from a dynein structure/mechanics review. review_file: genes/human/DYNC1H1/DYNC1H1-ai-review.yaml - organism: human gene: DYNC1H1 qualifier: involved_in term: id: GO:0090267 label: positive regulation of mitotic cell cycle spindle assembly checkpoint evidence: NAS reference: PMID:19229290 review_action: MODIFY review_summary: Positive regulation of mitotic spindle assembly checkpoint (NAS) from a LIC1 study. review_file: genes/human/DYNC1H1/DYNC1H1-ai-review.yaml - organism: human gene: DYNLT2B qualifier: part_of term: id: GO:0030286 label: dynein complex evidence: NAS reference: PMID:30065109 review_action: MODIFY review_summary: The established human complex is cytoplasmic dynein-2, rather than an unspecified dynein complex. review_file: genes/human/DYNLT2B/DYNLT2B-ai-review.yaml - organism: human gene: DYNLT2B qualifier: part_of term: id: GO:0030286 label: dynein complex evidence: NAS reference: PMID:32229580 review_action: MODIFY review_summary: The established human complex is cytoplasmic dynein-2, rather than an unspecified dynein complex. review_file: genes/human/DYNLT2B/DYNLT2B-ai-review.yaml - organism: human gene: E2F1 qualifier: involved_in term: id: GO:0006355 label: regulation of DNA-templated transcription evidence: IDA reference: PMID:1531329 review_action: MODIFY review_summary: 'Hiebert et al. 1992: formation of the E2F-pRB complex coincides with inhibition of E2F-dependent transcription from the adenovirus E2 promoter; a pRB mutant that cannot bind E2F does not inhibit. Classic demonstration that E2F is a transcription activator negatively regulated by RB1.' review_file: genes/human/E2F1/E2F1-ai-review.yaml - organism: human gene: E2F1 qualifier: involved_in term: id: GO:0006355 label: regulation of DNA-templated transcription evidence: IDA reference: PMID:23934193 review_action: MODIFY review_summary: Munro et al. 2014 show that cancer-associated DP-1 mutants transdominantly alter the DNA-binding, transactivation and pRB-binding properties of the E2F1/DP1 heterodimer and impair E2F1-dependent apoptosis - i.e. the heterodimer's transcriptional activity was assayed. review_file: genes/human/E2F1/E2F1-ai-review.yaml - organism: human gene: EIF4E2 qualifier: involved_in term: id: GO:1990261 label: pre-mRNA catabolic process evidence: NAS reference: PMID:33053355 review_action: MODIFY review_summary: ComplexPortal-derived annotation reflecting the 4EHP-GIGYF co-translational mRNA- decay complex. The biology is correct but 'pre-mRNA catabolic process' is imprecise; substrates are mature mRNAs. review_file: genes/human/EIF4E2/EIF4E2-ai-review.yaml - organism: human gene: FZR1 qualifier: involved_in term: id: GO:0007346 label: regulation of mitotic cell cycle evidence: NAS reference: PMID:15678131 review_action: MODIFY review_summary: Review-derived statement that APC/C-Cdh1 regulates the mitotic cell cycle. True but very general; the specific, well-evidenced cell-cycle role of FZR1 not otherwise captured is that APC/C-Cdh1 keeps cyclin A/SKP2/CDC6 and other S-phase promoters low during G1, so that Cdh1 overexpression imposes a G1 block and Cdh1 inactivation (CDK phosphorylation, Emi1) is required for S-phase entry. review_file: genes/human/FZR1/FZR1-ai-review.yaml - organism: human gene: GBA1 qualifier: involved_in term: id: GO:0019377 label: glycolipid catabolic process evidence: NAS reference: PMID:40159502 review_action: MODIFY review_summary: Glycolipid catabolic process is directionally correct but less specific than the supported GBA1 function. review_file: genes/human/GBA1/GBA1-ai-review.yaml - organism: human gene: GIGYF1 qualifier: involved_in term: id: GO:1990261 label: pre-mRNA catabolic process evidence: NAS reference: PMID:33053355 review_action: MODIFY review_summary: ComplexPortal-derived annotation reflecting GIGYF1's role in the 4EHP-GIGYF1 co-translational mRNA-decay complex. The biology (decay of mature, translated mRNAs that experience ribosome pausing) is correct, but 'pre-mRNA catabolic process' is an imprecise label, since the substrates are mature, ribosome-engaged mRNAs rather than pre-mRNA. review_file: genes/human/GIGYF1/GIGYF1-ai-review.yaml - organism: human gene: GIGYF2 qualifier: involved_in term: id: GO:1990261 label: pre-mRNA catabolic process evidence: NAS reference: PMID:33053355 review_action: MODIFY review_summary: ComplexPortal-derived annotation reflecting the 4EHP-GIGYF2 co-translational mRNA-decay complex. The biology (decay of translated, ribosome-stalled mRNAs) is correct, but 'pre-mRNA catabolic process' is imprecise; substrates are mature mRNAs. review_file: genes/human/GIGYF2/GIGYF2-ai-review.yaml - organism: human gene: GLI3 qualifier: involved_in term: id: GO:0006355 label: regulation of DNA-templated transcription evidence: IDA reference: PMID:24311597 review_action: MODIFY review_summary: Regulation of transcription attributed to GLI3 from the SUFU-GLI structure paper, which defines how SUFU engages the conserved SYGHL motif of GLI transcription factors and thereby modulates their activity. review_file: genes/human/GLI3/GLI3-ai-review.yaml - organism: human gene: GRPEL1 qualifier: involved_in term: id: GO:0006886 label: intracellular protein transport evidence: NAS reference: PMID:10339406 review_action: MODIFY review_summary: NAS annotation from ComplexPortal. GRPEL1 is involved in intracellular protein transport as part of the mitochondrial import machinery. However, this term is overly broad; the more specific term GO:0030150 (protein import into mitochondrial matrix) better captures GRPEL1's role. The cited paper (PMID:10339406) describes the TIM23 translocase but predates GRPEL1's identification. review_file: genes/human/GRPEL1/GRPEL1-ai-review.yaml - organism: human gene: HSPA9 qualifier: involved_in term: id: GO:0006886 label: intracellular protein transport evidence: NAS reference: PMID:10339406 review_action: MODIFY review_summary: Intracellular protein transport (ComplexPortal NAS) referring to HSPA9's role as the PAM motor of the TIM23 import machinery. The specific process is import of nuclear-encoded precursors into the mitochondrial matrix; the generic term is too broad. review_file: genes/human/HSPA9/HSPA9-ai-review.yaml - organism: human gene: IBA57 qualifier: involved_in term: id: GO:0051604 label: protein maturation evidence: NAS reference: PMID:31831856 review_action: MODIFY review_summary: IBA57 is involved in maturation of 4Fe-4S-containing proteins. The term protein maturation is correct but could be more specific. review_file: genes/human/IBA57/IBA57-ai-review.yaml - organism: human gene: INTU qualifier: located_in term: id: GO:0005929 label: cilium evidence: NAS reference: PMID:27158779 review_action: MODIFY review_summary: INTU localizes at the ciliary base/basal body rather than within the cilium proper. More specific term would be ciliary basal body. review_file: genes/human/INTU/INTU-ai-review.yaml - organism: human gene: INTU qualifier: involved_in term: id: GO:0042073 label: intraciliary transport evidence: NAS reference: PMID:27158779 review_action: MODIFY review_summary: 'This paper shows INTU recruits IFT-A machinery to basal bodies as part of the CPLANE complex. The newly cited PMID:35427153 shows CPLANE acts at the pre-ciliary vesicle stage with PI(3)P binding and CV-stage arrest, supporting an IFT-A recruitment / particle- assembly role rather than bidirectional axonemal cargo transport. Per PR #760 review feedback, downgraded ACCEPT → MODIFY with proposed replacement GO:0035735 (intraciliary transport particle assembly).' review_file: genes/human/INTU/INTU-ai-review.yaml - organism: human gene: INTU qualifier: involved_in term: id: GO:1902017 label: regulation of cilium assembly evidence: NAS reference: PMID:27158779 review_action: MODIFY review_summary: INTU is not just a regulator but is essential for cilium assembly itself. The more specific term cilium assembly (GO:0060271) better captures its essential role. review_file: genes/human/INTU/INTU-ai-review.yaml - organism: human gene: IRAK4 qualifier: involved_in term: id: GO:0044546 label: NLRP3 inflammasome complex assembly evidence: NAS reference: PMID:36865541 review_action: MODIFY review_summary: Review notes a role for IRAK4 and IRAK1 in non-transcriptional priming of the NLRP3 inflammasome. review_file: genes/human/IRAK4/IRAK4-ai-review.yaml - organism: human gene: KRAS qualifier: involved_in term: id: GO:0046579 label: positive regulation of Ras protein signal transduction evidence: NAS reference: PMID:35831509 review_action: MODIFY review_summary: This annotation captures KRAS-dependent positive signaling but frames the role as regulation of Ras signaling rather than direct participation in the Ras/MAPK pathway. review_file: genes/human/KRAS/KRAS-ai-review.yaml - organism: human gene: MCL1 qualifier: involved_in term: id: GO:0043065 label: positive regulation of apoptotic process evidence: IDA reference: PMID:21132008 review_action: MODIFY review_summary: This source supports MCL1 survival activity; the positive-apoptosis sign is wrong for long MCL1. review_file: genes/human/MCL1/MCL1-ai-review.yaml - organism: human gene: MYD88 qualifier: involved_in term: id: GO:0044546 label: NLRP3 inflammasome complex assembly evidence: NAS reference: PMID:36865541 review_action: MODIFY review_summary: 'NAS (IRAK review): NLRP3 inflammasome complex assembly.' review_file: genes/human/MYD88/MYD88-ai-review.yaml - organism: human gene: NDUFA4 qualifier: located_in term: id: GO:0031966 label: mitochondrial membrane evidence: IDA reference: PMID:30030519 review_action: MODIFY review_summary: NDUFA4 is specifically on the mitochondrial inner membrane. This term (mitochondrial membrane) is broader, encompassing both inner and outer membranes. review_file: genes/human/NDUFA4/NDUFA4-ai-review.yaml - organism: human gene: PAM16 qualifier: part_of term: id: GO:0005744 label: TIM23 mitochondrial import inner membrane translocase complex evidence: NAS reference: PMID:10339406 review_action: MODIFY review_summary: PAM16 is functionally coupled to TIM23, but its complex membership is more precisely the PAM import motor rather than the TIM23 channel/core translocase. review_file: genes/human/PAM16/PAM16-ai-review.yaml - organism: human gene: PDZD7 qualifier: involved_in term: id: GO:0060113 label: inner ear receptor cell differentiation evidence: NAS reference: PMID:25406310 review_action: MODIFY review_summary: ComplexPortal non-traceable author statement attached to the USH2 complex, citing the in vitro reconstitution paper. That paper is a biochemical study of complex assembly; the in vivo phenotype it summarizes for the four USH2 genes is disorganization and gradual degeneration of hair bundles, not a failure of hair-cell fate specification or of cell-type differentiation. review_file: genes/human/PDZD7/PDZD7-ai-review.yaml - organism: human gene: PIK3C3 qualifier: involved_in term: id: GO:0006622 label: protein targeting to lysosome evidence: NAS reference: PMID:16467569 review_action: MODIFY review_summary: Protein targeting to lysosome is a contextual trafficking assignment. review_file: genes/human/PIK3C3/PIK3C3-ai-review.yaml - organism: human gene: PIK3C3 qualifier: involved_in term: id: GO:0010506 label: regulation of autophagy evidence: IDA reference: PMID:16799551 review_action: MODIFY review_summary: This study supports PIK3C3 participation in macroautophagy, but classifying VPS34 itself as a regulator is too indirect. The gene product is part of the executing PI3KC3 complex. review_file: genes/human/PIK3C3/PIK3C3-ai-review.yaml - organism: human gene: PIK3C3 qualifier: involved_in term: id: GO:0016241 label: regulation of macroautophagy evidence: IDA reference: PMID:10625637 review_action: MODIFY review_summary: The underlying result supports macroautophagy itself rather than a purely regulatory role. PIK3C3 is required for the process. review_file: genes/human/PIK3C3/PIK3C3-ai-review.yaml - organism: human gene: PLN qualifier: involved_in term: id: GO:0051924 label: regulation of calcium ion transport evidence: IDA reference: PMID:26673394 review_action: MODIFY review_summary: IDA from GUV channel study. review_file: genes/human/PLN/PLN-ai-review.yaml - organism: human gene: PMAIP1 qualifier: involved_in term: id: GO:0043065 label: positive regulation of apoptotic process evidence: IDA reference: PMID:21132008 review_action: MODIFY review_summary: NOXA promotes apoptosis in the MCL1/BIM/BAK mitochondrial checkpoint. review_file: genes/human/PMAIP1/PMAIP1-ai-review.yaml - organism: human gene: PMPCA qualifier: located_in term: id: GO:0005739 label: mitochondrion evidence: NAS reference: PMID:32443488 review_action: MODIFY review_summary: PMPCA is mitochondrial, but the evidence supports the more specific mitochondrial matrix localization of the MPP machinery. review_file: genes/human/PMPCA/PMPCA-ai-review.yaml - organism: human gene: PPP3CA qualifier: involved_in term: id: GO:0070886 label: positive regulation of calcineurin-NFAT signaling cascade evidence: NAS reference: PMID:22343722 review_action: MODIFY review_summary: NAS assertion that PPP3CA positively regulates the calcineurin-NFAT signaling cascade. PPP3CA is the enzyme that executes this cascade (annotated as involved_in GO:0033173); it does not regulate it from outside. review_file: genes/human/PPP3CA/PPP3CA-ai-review.yaml - organism: human gene: PPP3CA qualifier: involved_in term: id: GO:0070886 label: positive regulation of calcineurin-NFAT signaling cascade evidence: NAS reference: PMID:8631904 review_action: MODIFY review_summary: NAS assertion of positive regulation of the calcineurin-NFAT cascade. The paper shows calcineurin directly binds and dephosphorylates NFAT1, i.e. PPP3CA is the cascade's catalytic step rather than a regulator. review_file: genes/human/PPP3CA/PPP3CA-ai-review.yaml - organism: human gene: PPP3CB qualifier: involved_in term: id: GO:0070886 label: positive regulation of calcineurin-NFAT signaling cascade evidence: NAS reference: PMID:22343722 review_action: MODIFY review_summary: Calcineurin does not regulate the calcineurin-NFAT cascade from outside; its NFAT phosphatase activity is the central step of the cascade. A positive-regulation term on the enzyme itself is a mis-framing; the appropriate term is calcineurin-NFAT signaling cascade (GO:0033173), which is also supported by IDA rows (PMID:19154138, PMID:22688515). Regulators of the cascade such as AKAP5 or NHE1 are the proper bearers of the regulation term. review_file: genes/human/PPP3CB/PPP3CB-ai-review.yaml - organism: human gene: PPP3CB qualifier: involved_in term: id: GO:0070886 label: positive regulation of calcineurin-NFAT signaling cascade evidence: NAS reference: PMID:8631904 review_action: MODIFY review_summary: Calcineurin does not regulate the calcineurin-NFAT cascade from outside; its NFAT phosphatase activity is the central step of the cascade. A positive-regulation term on the enzyme itself is a mis-framing; the appropriate term is calcineurin-NFAT signaling cascade (GO:0033173), which is also supported by IDA rows (PMID:19154138, PMID:22688515). Regulators of the cascade such as AKAP5 or NHE1 are the proper bearers of the regulation term. review_file: genes/human/PPP3CB/PPP3CB-ai-review.yaml - organism: human gene: PPP3R1 qualifier: involved_in term: id: GO:0070886 label: positive regulation of calcineurin-NFAT signaling cascade evidence: NAS reference: PMID:22343722 review_action: MODIFY review_summary: NAS positive regulation of calcineurin-NFAT signaling cascade. review_file: genes/human/PPP3R1/PPP3R1-ai-review.yaml - organism: human gene: PPP3R1 qualifier: involved_in term: id: GO:0070886 label: positive regulation of calcineurin-NFAT signaling cascade evidence: NAS reference: PMID:8631904 review_action: MODIFY review_summary: NAS positive regulation of calcineurin-NFAT signaling cascade. review_file: genes/human/PPP3R1/PPP3R1-ai-review.yaml - organism: human gene: RAD51B qualifier: involved_in term: id: GO:0097435 label: supramolecular fiber organization evidence: IDA reference: PMID:37344587 review_action: MODIFY review_summary: 'Supramolecular fiber organization (IDA): BCDX2 promotes RAD51 filament nucleation and extension.' review_file: genes/human/RAD51B/RAD51B-ai-review.yaml - organism: human gene: RAD51C qualifier: involved_in term: id: GO:0097435 label: supramolecular fiber organization evidence: IDA reference: PMID:37344587 review_action: MODIFY review_summary: As part of BCDX2, RAD51C promotes nucleation and extension of the RAD51 nucleoprotein filament (a supramolecular fiber) in an ATP-hydrolysis-dependent manner. This captures the core mediator function. review_file: genes/human/RAD51C/RAD51C-ai-review.yaml - organism: human gene: RAD51D qualifier: involved_in term: id: GO:0097435 label: supramolecular fiber organization evidence: IDA reference: PMID:37344587 review_action: MODIFY review_summary: 'Supramolecular fiber organization (IDA): BCDX2 promotes RAD51 filament nucleation and extension.' review_file: genes/human/RAD51D/RAD51D-ai-review.yaml - organism: human gene: RARA qualifier: involved_in term: id: GO:0042789 label: mRNA transcription by RNA polymerase II evidence: IDA reference: PMID:1310351 review_action: MODIFY review_summary: RARA regulates RNA polymerase II transcription rather than directly carrying out mRNA synthesis. review_file: genes/human/RARA/RARA-ai-review.yaml - organism: human gene: RARA qualifier: involved_in term: id: GO:0042789 label: mRNA transcription by RNA polymerase II evidence: NAS reference: PMID:9430642 review_action: MODIFY review_summary: RARA regulates RNA polymerase II transcription rather than directly carrying out mRNA synthesis. review_file: genes/human/RARA/RARA-ai-review.yaml - organism: human gene: RB1 qualifier: involved_in term: id: GO:0006355 label: regulation of DNA-templated transcription evidence: IDA reference: PMID:1531329 review_action: MODIFY review_summary: IDA annotation from Hiebert et al. 1992 (PMID:1531329, "The interaction of RB with E2F coincides with an inhibition of the transcriptional activity of E2F"), a canonical RB-E2F repression paper. Transfection assays of the adenovirus E2 promoter show that "formation of the complex containing pRB and E2F coincides with an inhibition of E2F-dependent transcriptional activity" and that "a mutant pRB protein that does not associate with E2F does not inhibit transcription." This directly demonstrates that RB1 *negatively* (not merely "regulates") regulates DNA-templated transcription. The generic parent GO:0006355 is too broad for this directional finding; the specific child GO:0045892 (negative regulation of DNA-templated transcription) is exactly what is shown, is already captured in core_functions[0].directly_involved_in, and is concordantly supported by IDA/TAS rows elsewhere in this file (PMID:12065415, PMID:10783144, PMID:19223331, PMID:19149898). review_file: genes/human/RB1/RB1-ai-review.yaml - organism: human gene: RBX1 qualifier: part_of term: id: GO:0000109 label: nucleotide-excision repair complex evidence: IPI reference: PMID:22118460 review_action: MODIFY review_summary: IPI row from the CRL4(DDB2)/CRL4(CSA) architecture study; the RBX1-containing entity characterised there is the DDB1-DDB2-CUL4A/B-RBX1 ubiquitin ligase, which acts in nucleotide-excision repair. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0051298 label: centrosome duplication evidence: NAS reference: PMID:34388369 review_action: MODIFY review_summary: NAS row for centrosome duplication; the cited reference is the cryo-EM structure of the human signal peptidase complex, which does not concern RBX1. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: SKP1 qualifier: involved_in term: id: GO:0051298 label: centrosome duplication evidence: NAS reference: PMID:34388369 review_action: MODIFY review_summary: 'Centrosome-duplication claim for SKP1: SCF(FBXW5) degrades HsSAS-6 and SCF(cyclin F) degrades CP110 to restrain centriole re-duplication, and anti-SKP1 antibodies blocked centriole separation in a cell-free system.' review_file: genes/human/SKP1/SKP1-ai-review.yaml - organism: human gene: SKP1 qualifier: involved_in term: id: GO:0060271 label: cilium assembly evidence: NAS reference: PMID:34368969 review_action: MODIFY review_summary: SCF(FBXW5) degrades the kinesin-13 depolymerases MCAK/KIF2C, KIF2A and KIF2B in G2; loss of FBXW5 raises MCAK at basal bodies and impairs ciliogenesis in the following G1/G0. review_file: genes/human/SKP1/SKP1-ai-review.yaml - organism: human gene: SLC3A1 qualifier: part_of term: id: GO:1902495 label: transmembrane transporter complex evidence: IPI reference: PMID:32494597 review_action: MODIFY review_summary: SLC3A1 is a heavy-chain component of the b0,+AT-rBAT amino-acid transport complex. review_file: genes/human/SLC3A1/SLC3A1-ai-review.yaml - organism: human gene: SLC7A11 qualifier: involved_in term: id: GO:0089718 label: amino acid import across plasma membrane evidence: IDA reference: PMID:11417227 review_action: MODIFY review_summary: IDA from functional characterization study. While correct, this is less specific than the available terms. review_file: genes/human/SLC7A11/SLC7A11-ai-review.yaml - organism: human gene: SSR1 qualifier: involved_in term: id: GO:0031204 label: post-translational protein targeting to membrane, translocation evidence: NAS reference: PMID:36697828 review_action: MODIFY review_summary: NAS annotation from ComplexPortal. However, this term refers to post-translational translocation, whereas TRAP is primarily involved in co-translational translocation. review_file: genes/human/SSR1/SSR1-ai-review.yaml - organism: human gene: STING1 qualifier: involved_in term: id: GO:0006914 label: autophagy evidence: NAS reference: PMID:40861013 review_action: MODIFY review_summary: The autophagy role of STING1 is specifically positive regulation of macroautophagy, which the gene already carries with experimental support. review_file: genes/human/STING1/STING1-ai-review.yaml - organism: human gene: STING1 qualifier: involved_in term: id: GO:0060340 label: positive regulation of type I interferon-mediated signaling pathway evidence: IDA reference: PMID:23910378 review_action: MODIFY review_summary: STING1 drives interferon production; it does not act within the interferon receptor signalling pathway. review_file: genes/human/STING1/STING1-ai-review.yaml - organism: human gene: STING1 qualifier: part_of term: id: GO:1902554 label: serine/threonine protein kinase complex evidence: NAS reference: PMID:24622840 review_action: MODIFY review_summary: The assembly meant here is the STING1-TBK1 signalosome, not a kinase complex of which STING1 is a subunit. review_file: genes/human/STING1/STING1-ai-review.yaml - organism: human gene: SUFU qualifier: involved_in term: id: GO:0006355 label: regulation of DNA-templated transcription evidence: IDA reference: PMID:24311597 review_action: MODIFY review_summary: Cherry et al. measured GLI1-driven reporter transcription in HEK 293 cells transfected with wild-type and interface-mutant SUFU constructs, showing that SUFU represses GLI activity and that specific interface residues are required for it. review_file: genes/human/SUFU/SUFU-ai-review.yaml - organism: human gene: SUN1 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:38291267 review_action: MODIFY review_summary: Meiotic LINC complex (IPI) from the SUN1-KASH6 (JAW1/LRMP) crystal structure. review_file: genes/human/SUN1/SUN1-ai-review.yaml - organism: human gene: SUN1 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:22632968 review_action: MODIFY review_summary: Meiotic LINC complex (IPI) from the SUN2-KASH1/2 crystal structure paper. review_file: genes/human/SUN1/SUN1-ai-review.yaml - organism: human gene: SUN1 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:33058875 review_action: MODIFY review_summary: Meiotic LINC complex (IPI) from SUN2 structures with nesprin-3, nesprin-4 and KASH5 peptides. review_file: genes/human/SUN1/SUN1-ai-review.yaml - organism: human gene: SUN2 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:22632968 review_action: MODIFY review_summary: Crystal structure of SUN2 with nesprin-1/2 KASH peptides. review_file: genes/human/SUN2/SUN2-ai-review.yaml - organism: human gene: SUN2 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:33393904 review_action: MODIFY review_summary: SUN2-KASH 6:6 assemblies including KASH5. review_file: genes/human/SUN2/SUN2-ai-review.yaml - organism: human gene: SUN2 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:33058875 review_action: MODIFY review_summary: Crystal structures of SUN2 with KASH peptides including KASH5, the meiotic KASH protein. review_file: genes/human/SUN2/SUN2-ai-review.yaml - organism: human gene: SYCE3 qualifier: involved_in term: id: GO:0035825 label: homologous recombination evidence: NAS reference: PMID:27142324 review_action: MODIFY review_summary: Homologous recombination is a very broad term that encompasses both mitotic and meiotic recombination. For SYCE3, the more specific term GO:0007131 (reciprocal meiotic recombination) is more appropriate. review_file: genes/human/SYCE3/SYCE3-ai-review.yaml - organism: human gene: SYNE1 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:22632968 review_action: MODIFY review_summary: Meiotic nuclear membrane microtubule tethering complex (LINC complex). review_file: genes/human/SYNE1/SYNE1-ai-review.yaml - organism: human gene: SYNE1 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:33393904 review_action: MODIFY review_summary: Meiotic nuclear membrane microtubule tethering complex (LINC complex). review_file: genes/human/SYNE1/SYNE1-ai-review.yaml - organism: human gene: SYNE2 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:22632968 review_action: MODIFY review_summary: Part of meiotic LINC complex (IPI); SUN2-KASH2 heterohexamer structure. review_file: genes/human/SYNE2/SYNE2-ai-review.yaml - organism: human gene: SYNE3 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:33058875 review_action: MODIFY review_summary: Crystal structure of SUN2 in complex with the nesprin-3 KASH peptide. review_file: genes/human/SYNE3/SYNE3-ai-review.yaml - organism: human gene: SYNE4 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:33058875 review_action: MODIFY review_summary: Crystal structure of SUN2 bound to the nesprin-4 KASH peptide. review_file: genes/human/SYNE4/SYNE4-ai-review.yaml - organism: human gene: TEAD1 qualifier: involved_in term: id: GO:0030307 label: positive regulation of cell growth evidence: IDA reference: PMID:18579750 review_action: MODIFY review_summary: 'Zhao et al. 2008: TEAD1-YAP-S94A fusion stimulates NIH-3T3 cell growth (cell number) and rescues target gene expression.' review_file: genes/human/TEAD1/TEAD1-ai-review.yaml - organism: human gene: TIMM17A qualifier: involved_in term: id: GO:0006886 label: intracellular protein transport evidence: NAS reference: PMID:10339406 review_action: MODIFY review_summary: The annotation captures protein transport but is too broad. The specific TIMM17A process is mitochondrial matrix import through TIM23. review_file: genes/human/TIMM17A/TIMM17A-ai-review.yaml - organism: human gene: TIMM44 qualifier: part_of term: id: GO:0005744 label: TIM23 mitochondrial import inner membrane translocase complex evidence: NAS reference: PMID:10339406 review_action: MODIFY review_summary: TIMM44 is functionally coupled to TIM23, but the more precise complex term is PAM complex rather than the TIM23 translocase core complex. review_file: genes/human/TIMM44/TIMM44-ai-review.yaml - organism: human gene: TLN1 qualifier: involved_in term: id: GO:0051893 label: regulation of focal adhesion assembly evidence: NAS reference: PMID:15070891 review_action: MODIFY review_summary: NAS regulation of focal adhesion assembly, from the talin-vinculin structural study. review_file: genes/human/TLN1/TLN1-ai-review.yaml - organism: human gene: TOMM40 qualifier: involved_in term: id: GO:0045040 label: protein insertion into mitochondrial outer membrane evidence: NAS reference: PMID:18331822 review_action: MODIFY review_summary: This term refers to insertion of proteins INTO the outer membrane (e.g., alpha-helical or beta-barrel proteins). TOMM40 itself is inserted into the OM but does not catalyze insertion of others — that is the role of SAM (for beta-barrels) and MTCH2/MIM (for alpha-helical proteins). TOMM40 facilitates translocation THROUGH the outer membrane, not insertion into it. review_file: genes/human/TOMM40/TOMM40-ai-review.yaml - organism: human gene: TOMM5 qualifier: involved_in term: id: GO:0045040 label: protein insertion into mitochondrial outer membrane evidence: NAS reference: PMID:18331822 review_action: MODIFY review_summary: TOMM5 supports TOM organization and biogenesis, but the evidence does not support TOMM5 as an independent insertase for outer membrane proteins. TOM complex assembly is the more precise process annotation. review_file: genes/human/TOMM5/TOMM5-ai-review.yaml - organism: human gene: TOMM6 qualifier: involved_in term: id: GO:0045040 label: protein insertion into mitochondrial outer membrane evidence: NAS reference: PMID:18331822 review_action: MODIFY review_summary: The broad direction of the annotation is related to TOMM6 biology, but TOMM6 is not itself an insertase. Evidence better supports a role in TOM core assembly, stability, and oligomerization. review_file: genes/human/TOMM6/TOMM6-ai-review.yaml - organism: human gene: TOMM7 qualifier: involved_in term: id: GO:0045040 label: protein insertion into mitochondrial outer membrane evidence: NAS reference: PMID:18331822 review_action: MODIFY review_summary: The broad TOM biology is related, but TOMM7 is not an independent insertase. The specific supported role is TOM complex assembly/stability and oligomeric-state regulation. review_file: genes/human/TOMM7/TOMM7-ai-review.yaml - organism: human gene: TOMM70 qualifier: involved_in term: id: GO:0045040 label: protein insertion into mitochondrial outer membrane evidence: NAS reference: PMID:18331822 review_action: MODIFY review_summary: The annotation captures mitochondrial protein import context but overstates TOMM70 as an outer-membrane insertase. review_file: genes/human/TOMM70/TOMM70-ai-review.yaml - organism: human gene: TRAPPC1 qualifier: involved_in term: id: GO:0006901 label: vesicle coat assembly evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: TRAPPC complexes interact with vesicle coats and RAB1 on ER-derived vesicles, but TRAPPC1 is not a coat-assembly factor. review_file: genes/human/TRAPPC1/TRAPPC1-ai-review.yaml - organism: human gene: TRAPPC1 qualifier: involved_in term: id: GO:0048208 label: COPII vesicle coat assembly evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: The COPII evidence places TRAPPCII near SEC23/COPII vesicles, but does not show TRAPPC1 assembling the COPII coat. review_file: genes/human/TRAPPC1/TRAPPC1-ai-review.yaml - organism: human gene: TRAPPC1 qualifier: involved_in term: id: GO:0099022 label: obsolete vesicle tethering evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: This annotation uses an obsolete vesicle-tethering term, and the cited TRAPP review cautions that direct TRAPP tethering evidence is inconclusive. review_file: genes/human/TRAPPC1/TRAPPC1-ai-review.yaml - organism: human gene: TRAPPC11 qualifier: involved_in term: id: GO:0048208 label: COPII vesicle coat assembly evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: The COPII coat assembly annotation captures early secretory context but overstates TRAPPC11 as a coat-assembly factor. review_file: genes/human/TRAPPC11/TRAPPC11-ai-review.yaml - organism: human gene: TRAPPC11 qualifier: involved_in term: id: GO:0099022 label: obsolete vesicle tethering evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: The obsolete vesicle-tethering annotation should not be retained as-is. review_file: genes/human/TRAPPC11/TRAPPC11-ai-review.yaml - organism: human gene: TRAPPC12 qualifier: involved_in term: id: GO:0048208 label: COPII vesicle coat assembly evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: The COPII coat assembly annotation captures early secretory context but overstates TRAPPC12 as a coat-assembly factor. review_file: genes/human/TRAPPC12/TRAPPC12-ai-review.yaml - organism: human gene: TRAPPC12 qualifier: involved_in term: id: GO:0099022 label: obsolete vesicle tethering evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: The obsolete vesicle-tethering annotation should not be retained as-is. review_file: genes/human/TRAPPC12/TRAPPC12-ai-review.yaml - organism: human gene: TRAPPC13 qualifier: involved_in term: id: GO:0006901 label: vesicle coat assembly evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: The coat-assembly annotation captures COPII-associated transport context but overstates TRAPPC13 as a coat assembly factor. review_file: genes/human/TRAPPC13/TRAPPC13-ai-review.yaml - organism: human gene: TRAPPC13 qualifier: involved_in term: id: GO:0099022 label: obsolete vesicle tethering evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: The obsolete vesicle-tethering annotation should not be retained as-is. review_file: genes/human/TRAPPC13/TRAPPC13-ai-review.yaml - organism: human gene: TRAPPC3 qualifier: involved_in term: id: GO:0006901 label: vesicle coat assembly evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: TRAPPC3 interacts with COPII/SEC23-associated ER-derived vesicle trafficking machinery, but it is not a vesicle coat assembly factor. review_file: genes/human/TRAPPC3/TRAPPC3-ai-review.yaml - organism: human gene: TRAPPC3 qualifier: involved_in term: id: GO:0048208 label: COPII vesicle coat assembly evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: The COPII evidence supports TRAPPC3-SEC23 recruitment to ER-derived vesicles, not direct COPII coat assembly by TRAPPC3. review_file: genes/human/TRAPPC3/TRAPPC3-ai-review.yaml - organism: human gene: TRAPPC3 qualifier: involved_in term: id: GO:0099022 label: obsolete vesicle tethering evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: This obsolete vesicle-tethering annotation should not be kept as-is, and direct mammalian TRAPP tethering evidence remains unresolved. review_file: genes/human/TRAPPC3/TRAPPC3-ai-review.yaml - organism: human gene: TRAPPC4 qualifier: involved_in term: id: GO:0006901 label: vesicle coat assembly evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: vesicle coat assembly overstates TRAPPC4 as a coat-assembly factor. review_file: genes/human/TRAPPC4/TRAPPC4-ai-review.yaml - organism: human gene: TRAPPC4 qualifier: involved_in term: id: GO:0048208 label: COPII vesicle coat assembly evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: COPII vesicle coat assembly overstates TRAPPC4 as a coat-assembly factor. review_file: genes/human/TRAPPC4/TRAPPC4-ai-review.yaml - organism: human gene: TRAPPC4 qualifier: involved_in term: id: GO:0099022 label: obsolete vesicle tethering evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: The obsolete vesicle-tethering annotation should not be retained as-is. review_file: genes/human/TRAPPC4/TRAPPC4-ai-review.yaml - organism: human gene: TRAPPC5 qualifier: involved_in term: id: GO:0006901 label: vesicle coat assembly evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: vesicle coat assembly overstates TRAPPC5 as a coat-assembly factor. review_file: genes/human/TRAPPC5/TRAPPC5-ai-review.yaml - organism: human gene: TRAPPC5 qualifier: involved_in term: id: GO:0048208 label: COPII vesicle coat assembly evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: COPII vesicle coat assembly overstates TRAPPC5 as a coat-assembly factor. review_file: genes/human/TRAPPC5/TRAPPC5-ai-review.yaml - organism: human gene: TRAPPC5 qualifier: involved_in term: id: GO:0099022 label: obsolete vesicle tethering evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: The obsolete vesicle-tethering annotation should not be kept as-is for TRAPPC5. review_file: genes/human/TRAPPC5/TRAPPC5-ai-review.yaml - organism: human gene: TRAPPC8 qualifier: involved_in term: id: GO:0048208 label: COPII vesicle coat assembly evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: The COPII annotation captures cargo transport context but overstates TRAPPC8 as a coat-assembly factor. review_file: genes/human/TRAPPC8/TRAPPC8-ai-review.yaml - organism: human gene: TRAPPC8 qualifier: involved_in term: id: GO:0099022 label: obsolete vesicle tethering evidence: NAS reference: PMID:27066478 review_action: MODIFY review_summary: The obsolete vesicle-tethering annotation should not be retained as-is. review_file: genes/human/TRAPPC8/TRAPPC8-ai-review.yaml - organism: human gene: UVRAG qualifier: involved_in term: id: GO:0010506 label: regulation of autophagy evidence: IDA reference: PMID:16799551 review_action: MODIFY review_summary: UVRAG positively regulates Beclin1-PI3KC3 autophagy activity, so the undirected regulation term should be narrowed. review_file: genes/human/UVRAG/UVRAG-ai-review.yaml - organism: human gene: UVRAG qualifier: part_of term: id: GO:0035032 label: phosphatidylinositol 3-kinase complex, class III evidence: IPI reference: PMID:25490155 review_action: MODIFY review_summary: Generic class III PI3K complex membership is correct but underspecified for UVRAG. review_file: genes/human/UVRAG/UVRAG-ai-review.yaml - organism: human gene: WHRN qualifier: involved_in term: id: GO:0060113 label: inner ear receptor cell differentiation evidence: NAS reference: PMID:25406310 review_action: MODIFY review_summary: NAS annotation from the USH2 quaternary complex paper, which states (citing prior work) that the four USH2 genes are important for hair cell development. Whirlin's contribution to hair-cell development is specifically through stereocilium bundle morphogenesis rather than cell differentiation per se. review_file: genes/human/WHRN/WHRN-ai-review.yaml - organism: human gene: XBP1 qualifier: involved_in term: id: GO:0036503 label: ERAD quality control pathway evidence: NAS reference: PMID:17765680 review_action: MODIFY review_summary: ATF6alpha heterodimerizes with XBP1 to induce ERAD components (PMID:17765680). review_file: genes/human/XBP1/XBP1-ai-review.yaml - organism: human gene: XRCC2 qualifier: involved_in term: id: GO:0097435 label: supramolecular fiber organization evidence: IDA reference: PMID:37344587 review_action: MODIFY review_summary: 'Captures BCDX2''s mediator activity: promoting the nucleation and extension of RAD51 nucleoprotein filaments (supramolecular fibers) on ssDNA.' review_file: genes/human/XRCC2/XRCC2-ai-review.yaml - organism: mouse gene: Myc qualifier: involved_in term: id: GO:0045893 label: positive regulation of DNA-templated transcription evidence: IDA reference: PMID:20434984 review_action: MODIFY review_summary: PMID:20434984 supports Myc regulation of Pol II promoter-proximal pause release rather than a broad transcription-positive-regulation assertion. review_file: genes/mouse/Myc/Myc-ai-review.yaml - organism: worm gene: atg-13 qualifier: part_of term: id: GO:1902554 label: serine/threonine protein kinase complex evidence: NAS reference: PMID:19377305 review_action: MODIFY review_summary: EPG-1 is in a complex with the UNC-51 kinase. review_file: genes/worm/atg-13/atg-13-ai-review.yaml - organism: worm gene: atg-16.2 qualifier: located_in term: id: GO:0034045 label: obsolete phagophore assembly site membrane evidence: NAS reference: PMID:24185444 review_action: MODIFY review_summary: Author statement mapped to the now-obsolete PAS membrane term. review_file: genes/worm/atg-16.2/atg-16.2-ai-review.yaml - organism: worm gene: atg-5 qualifier: located_in term: id: GO:0034045 label: obsolete phagophore assembly site membrane evidence: NAS reference: PMID:24185444 review_action: MODIFY review_summary: Author statement mapped to the now-obsolete PAS membrane term. review_file: genes/worm/atg-5/atg-5-ai-review.yaml - organism: worm gene: atg-5 qualifier: part_of term: id: GO:1990234 label: transferase complex evidence: NAS reference: PMID:24185444 review_action: MODIFY review_summary: Author statement mapped to transferase complex. review_file: genes/worm/atg-5/atg-5-ai-review.yaml - organism: worm gene: ced-4 qualifier: involved_in term: id: GO:0043065 label: positive regulation of apoptotic process evidence: EXP reference: PMID:10846174 review_action: MODIFY review_summary: CED-4 acts in the apoptotic signaling step that activates the CED-3 zymogen. review_file: genes/worm/ced-4/ced-4-ai-review.yaml - organism: worm gene: ced-9 qualifier: involved_in term: id: GO:0043065 label: positive regulation of apoptotic process evidence: EXP reference: PMID:10846174 review_action: MODIFY review_summary: The cited EGL-1 experiment establishes that EGL-1 relieves the inhibitory CED-9/CED-4 complex. review_file: genes/worm/ced-9/ced-9-ai-review.yaml - organism: worm gene: cep-1 qualifier: involved_in term: id: GO:0008630 label: intrinsic apoptotic signaling pathway in response to DNA damage evidence: IMP reference: PMID:19521535 review_action: MODIFY review_summary: The PRMT-5/CBP-1 evidence concerns CEP-1-dependent DNA-damage apoptosis and can be represented with the p53-class mediator child term. review_file: genes/worm/cep-1/cep-1-ai-review.yaml - organism: worm gene: che-2 qualifier: involved_in term: id: GO:0042073 label: intraciliary transport evidence: NAS reference: PMID:28479320 review_action: MODIFY review_summary: CHE-2 as an IFT-B component participates in intraciliary transport. PMID:28479320 focuses on retrograde IFT but discusses the overall IFT machinery including IFT-B. PMID:22922713 provides more detailed evidence of CHE-2 orthologs' IFT movement. review_file: genes/worm/che-2/che-2-ai-review.yaml - organism: worm gene: daf-18 qualifier: involved_in term: id: GO:0046628 label: positive regulation of insulin receptor signaling pathway evidence: NAS reference: PMID:20207731 review_action: MODIFY review_summary: NAS positive regulation of insulin receptor signaling pathway (Palmitessa & Benovic 2010, ARR-1/MPZ-1/DAF-18 complex). review_file: genes/worm/daf-18/daf-18-ai-review.yaml - organism: worm gene: lag-1 qualifier: involved_in term: id: GO:0045893 label: positive regulation of DNA-templated transcription evidence: NAS reference: PMID:16530045 review_action: MODIFY review_summary: ComplexPortal NAS for positive regulation of transcription by the CSL-Notch-Mastermind complex. review_file: genes/worm/lag-1/lag-1-ai-review.yaml - organism: worm gene: lis-1 qualifier: involved_in term: id: GO:0031022 label: nuclear migration along microfilament evidence: IMP reference: PMID:20005871 review_action: MODIFY review_summary: lis-1(RNAi) causes hyp7 nuclear migration defects; NUD-2/LIS-1 is recruited to the nuclear envelope by UNC-83. review_file: genes/worm/lis-1/lis-1-ai-review.yaml - organism: worm gene: nud-2 qualifier: involved_in term: id: GO:0031022 label: nuclear migration along microfilament evidence: IMP reference: PMID:20005871 review_action: MODIFY review_summary: nud-2 mutant hyp7 nuclear migration defect, annotated as nuclear migration along microfilament. review_file: genes/worm/nud-2/nud-2-ai-review.yaml - organism: worm gene: sel-8 qualifier: involved_in term: id: GO:0045893 label: positive regulation of DNA-templated transcription evidence: NAS reference: PMID:16530045 review_action: MODIFY review_summary: ComplexPortal NAS for positive regulation of transcription by the CSL-Notch-Mastermind complex. review_file: genes/worm/sel-8/sel-8-ai-review.yaml - organism: worm gene: unc-51 qualifier: part_of term: id: GO:1902554 label: serine/threonine protein kinase complex evidence: NAS reference: PMID:19377305 review_action: MODIFY review_summary: UNC-51 forms a complex with EPG-1/ATG-13. review_file: genes/worm/unc-51/unc-51-ai-review.yaml - organism: worm gene: unc-83 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:16481402 review_action: MODIFY review_summary: UNC-83-UNC-84 SUN-KASH complex. review_file: genes/worm/unc-83/unc-83-ai-review.yaml - organism: worm gene: unc-84 qualifier: part_of term: id: GO:0034993 label: meiotic nuclear membrane microtubule tethering complex evidence: IPI reference: PMID:16481402 review_action: MODIFY review_summary: UNC-84-UNC-83 SUN-KASH complex spanning the nuclear envelope. review_file: genes/worm/unc-84/unc-84-ai-review.yaml - organism: yeast gene: APC11 qualifier: involved_in term: id: GO:0007346 label: regulation of mitotic cell cycle evidence: NAS reference: PMID:16481473 review_action: MODIFY review_summary: 'ComplexPortal NAS row attached to the APC/C core complex (CPX-756) citing Thornton et al. 2006. The statement is true but shallow: the APC/C does not merely modulate the mitotic cycle, it executes two irreversible transitions by ubiquitinating securin and the B-type cyclins, which the paper identifies as the only obligatory APC/C targets, and Apc11 is the RING subunit that catalyses that ubiquitination.' review_file: genes/yeast/APC11/APC11-ai-review.yaml - organism: yeast gene: APC2 qualifier: involved_in term: id: GO:0007346 label: regulation of mitotic cell cycle evidence: NAS reference: PMID:16481473 review_action: MODIFY review_summary: 'ComplexPortal NAS row attached to the APC/C core complex (CPX-756) citing Thornton et al. 2006. The statement is true but shallow: the APC/C does not merely modulate the mitotic cycle, it executes two irreversible transitions by ubiquitinating securin and B-type cyclins, which the paper identifies as the only obligatory APC/C targets.' review_file: genes/yeast/APC2/APC2-ai-review.yaml - organism: yeast gene: CAC2 qualifier: involved_in term: id: GO:0006325 label: chromatin organization evidence: IDA reference: PMID:30239791 review_action: MODIFY review_summary: Complex Portal annotation of CAC2/CAF-1 to the general process chromatin organization. review_file: genes/yeast/CAC2/CAC2-ai-review.yaml - organism: yeast gene: CDC16 qualifier: involved_in term: id: GO:0007346 label: regulation of mitotic cell cycle evidence: NAS reference: PMID:16481473 review_action: MODIFY review_summary: ComplexPortal NAS attached to the whole APC/C (CPX-756) from the architectural study of Thornton et al. 2006. The APC/C ubiquitinates securin and the mitotic cyclins, triggering the metaphase-to-anaphase transition and exit from mitosis; APC/C lacking Cdc16 has no activity. review_file: genes/yeast/CDC16/CDC16-ai-review.yaml - organism: yeast gene: CDC20 qualifier: involved_in term: id: GO:0007346 label: regulation of mitotic cell cycle evidence: NAS reference: PMID:16481473 review_action: MODIFY review_summary: Generic regulatory term attached to the APC architecture paper; Cdc20's regulatory role is specifically the activation of APC/C at the metaphase/anaphase transition. review_file: genes/yeast/CDC20/CDC20-ai-review.yaml - organism: yeast gene: CDC20 qualifier: involved_in term: id: GO:0016567 label: protein ubiquitination evidence: NAS reference: PMID:16481473 review_action: MODIFY review_summary: General ubiquitination process term from the APC architecture paper; Cdc20 does not catalyse ubiquitin transfer but activates and directs the APC/C ligase. review_file: genes/yeast/CDC20/CDC20-ai-review.yaml - organism: yeast gene: CDC28 qualifier: involved_in term: id: GO:1902806 label: regulation of cell cycle G1/S phase transition evidence: NAS reference: PMID:2569741 review_action: MODIFY review_summary: Hadwiger et al. isolated CLN1/CLN2 as dosage suppressors of cdc28-ts, defining the G1 cyclins that act with Cdc28 at Start. review_file: genes/yeast/CDC28/CDC28-ai-review.yaml - organism: yeast gene: CDC4 qualifier: involved_in term: id: GO:0006511 label: ubiquitin-dependent protein catabolic process evidence: IDA reference: PMID:14747994 review_action: MODIFY review_summary: Cdc4 mediates ubiquitin-dependent proteolysis as the substrate receptor of the SCF(Cdc4) ligase that ubiquitinates phosphorylated Sic1 for proteasomal destruction. review_file: genes/yeast/CDC4/CDC4-ai-review.yaml - organism: yeast gene: CDC53 qualifier: involved_in term: id: GO:0007346 label: regulation of mitotic cell cycle evidence: NAS reference: PMID:12150908 review_action: MODIFY review_summary: Broad cell-cycle regulation term attached to a paper on SCF(Met30) control of the Met4 transcription factor; Cdc53 regulates the mitotic cell cycle specifically through SCF(Cdc4)/SCF(Grr1) destruction of Sic1 and the G1 cyclins at the G1/S transition. review_file: genes/yeast/CDC53/CDC53-ai-review.yaml - organism: yeast gene: CDC53 qualifier: involved_in term: id: GO:0031573 label: mitotic intra-S DNA damage checkpoint signaling evidence: NAS reference: PMID:23172854 review_action: MODIFY review_summary: SCF(Dia2) mediates Mrc1 degradation during recovery from MMS-induced replication stress, promoting deactivation of Rad53 and resumption of the cell cycle; Cdc53 is the cullin of that ligase. review_file: genes/yeast/CDC53/CDC53-ai-review.yaml - organism: yeast gene: CLN2 qualifier: involved_in term: id: GO:1902806 label: regulation of cell cycle G1/S phase transition evidence: NAS reference: PMID:2569741 review_action: MODIFY review_summary: Complex Portal author-statement annotation (for the CLN2-CDC28 kinase complex, CPX-342) citing the Hadwiger et al. 1989 cloning paper. The complex does regulate the G1/S transition, but the term is the generic, direction-less parent and is not specific to the mitotic cycle. review_file: genes/yeast/CLN2/CLN2-ai-review.yaml - organism: yeast gene: CLN3 qualifier: involved_in term: id: GO:1902806 label: regulation of cell cycle G1/S phase transition evidence: NAS reference: PMID:2569741 review_action: MODIFY review_summary: Author-statement annotation citing Hadwiger et al. 1989, the paper that cloned CLN1 and CLN2 as cyclin homologs and dosage suppressors of cdc28-ts; CLN3 (then WHI1/DAF1) is discussed as the third family member. Cln3 does modulate the G1/S CDK switch, and it does so positively. review_file: genes/yeast/CLN3/CLN3-ai-review.yaml - organism: yeast gene: HRT1 qualifier: involved_in term: id: GO:0006289 label: nucleotide-excision repair evidence: NAS reference: PMID:17296727 review_action: MODIFY review_summary: Elc1, Ela1 and Cul3 are required for K48-polyubiquitylation and degradation of Rpb1 in DNA-damaged cells, and the authors propose an Elc1-Ela1-Cul3-Roc1 ligase; they also show that Pol II degradation is not a prerequisite for Rad26-dependent transcription-coupled repair but a separate route to lesion removal. review_file: genes/yeast/HRT1/HRT1-ai-review.yaml - organism: yeast gene: HRT1 qualifier: involved_in term: id: GO:0007346 label: regulation of mitotic cell cycle evidence: NAS reference: PMID:12150908 review_action: MODIFY review_summary: Broad cell-cycle regulation term attached to a paper on SCF(Met30) control of the Met4 transcription factor; Hrt1 regulates the mitotic cell cycle specifically through SCF(Cdc4)/SCF(Grr1) destruction of Sic1 and the G1 cyclins at the G1/S transition. review_file: genes/yeast/HRT1/HRT1-ai-review.yaml - organism: yeast gene: HRT1 qualifier: involved_in term: id: GO:0031573 label: mitotic intra-S DNA damage checkpoint signaling evidence: NAS reference: PMID:23172854 review_action: MODIFY review_summary: SCF(Dia2) mediates Mrc1 degradation during recovery from MMS-induced replication stress, promoting Rad53 deactivation and resumption of the cell cycle; Hrt1 is the RING of that ligase. review_file: genes/yeast/HRT1/HRT1-ai-review.yaml - organism: yeast gene: MBP1 qualifier: involved_in term: id: GO:0006355 label: regulation of DNA-templated transcription evidence: NAS reference: PMID:8372350 review_action: MODIFY review_summary: Complex Portal-sourced author statement from Koch et al. 1993 that MBF regulates MCB-driven transcription of DNA-synthesis genes. review_file: genes/yeast/MBP1/MBP1-ai-review.yaml - organism: yeast gene: MIM1 qualifier: involved_in term: id: GO:0045040 label: protein insertion into mitochondrial outer membrane evidence: IDA reference: PMID:32348752 review_action: MODIFY review_summary: ComplexPortal IDA from the study that defined the MIM complex as the main translocase for alpha-helical outer-membrane proteins. Beyond the multi-spanning substrates already known, this work showed that MIM inserts both N-terminally (signal-anchored) and C-terminally (tail-anchored) single-spanning precursors, described three dynamic populations of the complex (TOM-associated, free, SAM-coupled), and concluded that MIM is a major and versatile protein translocase of the outer membrane. review_file: genes/yeast/MIM1/MIM1-ai-review.yaml - organism: yeast gene: MSI1 qualifier: involved_in term: id: GO:0006325 label: chromatin organization evidence: IDA reference: PMID:30239791 review_action: MODIFY review_summary: Complex Portal annotation of MSI1/CAF-1 to the general process chromatin organization. review_file: genes/yeast/MSI1/MSI1-ai-review.yaml - organism: yeast gene: POB3 qualifier: involved_in term: id: GO:1902275 label: regulation of chromatin organization evidence: NAS reference: PMID:12952948 review_action: MODIFY review_summary: NAS evidence from ComplexPortal annotation. FACT dynamically reorganizes chromatin structure in response to transcriptional and replicational demands. However, POB3 is not a regulatory protein per se, but rather an executor of nucleosome dynamics. review_file: genes/yeast/POB3/POB3-ai-review.yaml - organism: yeast gene: RLF2 qualifier: involved_in term: id: GO:0006325 label: chromatin organization evidence: IDA reference: PMID:30239791 review_action: MODIFY review_summary: Complex Portal annotation of RLF2/CAF-1 to the general process chromatin organization. review_file: genes/yeast/RLF2/RLF2-ai-review.yaml - organism: yeast gene: SKP1 qualifier: involved_in term: id: GO:0007346 label: regulation of mitotic cell cycle evidence: NAS reference: PMID:12150908 review_action: MODIFY review_summary: ComplexPortal author-statement row for SCF(Met30), whose cited paper concerns ubiquitylation-dependent and -independent inhibition of the Met4 activator rather than cell-cycle control. review_file: genes/yeast/SKP1/SKP1-ai-review.yaml - organism: yeast gene: SKP1 qualifier: involved_in term: id: GO:0031573 label: mitotic intra-S DNA damage checkpoint signaling evidence: NAS reference: PMID:23172854 review_action: MODIFY review_summary: 'ComplexPortal row for SCF(Dia2): Dia2 is needed for robust Rad53 deactivation and Mrc1 degradation during recovery from MMS damage, i.e. for switching the S-phase checkpoint off.' review_file: genes/yeast/SKP1/SKP1-ai-review.yaml - organism: yeast gene: SWI4 qualifier: involved_in term: id: GO:0006355 label: regulation of DNA-templated transcription evidence: IMP reference: PMID:18268013 review_action: MODIFY review_summary: 'Kim, Truman and Levin 2008 (abstract-only cache; ComplexPortal-sourced IMP): cell-wall stress induction of FKS2 requires SBF and an activating signal to Mpk1 but not Mpk1 catalytic activity; phosphorylated Mpk1 (or Mlp1) is found with Swi4 and Swi6 at the FKS2 promoter, Mpk1 and Swi4 promoter association are codependent and Swi6-independent, and Swi6 is then recruited to activate transcription.' review_file: genes/yeast/SWI4/SWI4-ai-review.yaml - organism: yeast gene: SWI6 qualifier: involved_in term: id: GO:0006355 label: regulation of DNA-templated transcription evidence: IMP reference: PMID:18268013 review_action: MODIFY review_summary: 'Kim, Truman and Levin 2008 (abstract-only cache; ComplexPortal-sourced IMP): cell-wall stress induction of FKS2 requires SBF and an activating signal to Mpk1 but not Mpk1 catalytic activity; phosphorylated Mpk1 (or Mlp1) is found with Swi4 and Swi6 at the FKS2 promoter, Swi4 promoter binding is Swi6-independent, and Swi6 is then recruited to the Swi4-Mpk1 complex to activate transcription.' review_file: genes/yeast/SWI6/SWI6-ai-review.yaml - organism: yeast gene: SWI6 qualifier: involved_in term: id: GO:0006355 label: regulation of DNA-templated transcription evidence: NAS reference: PMID:8372350 review_action: MODIFY review_summary: 'Koch et al. 1993 (abstract-only cache): statement-level annotation that Swi6, as a subunit of SBF and MBF, regulates transcription; the paper shows SBF activates G1 cyclin genes and MBF directly regulates MCB-driven transcription of DNA-synthesis genes.' review_file: genes/yeast/SWI6/SWI6-ai-review.yaml - organism: DROME gene: aub qualifier: involved_in term: id: GO:1900370 label: positive regulation of post-transcriptional gene silencing by RNA evidence: IDA reference: PMID:19959991 review_action: MARK_AS_OVER_ANNOTATED review_summary: Positive regulation of PTGS by RNA (PMID:19959991). review_file: genes/DROME/aub/aub-ai-review.yaml - organism: DROME gene: fu qualifier: involved_in term: id: GO:0000122 label: negative regulation of transcription by RNA polymerase II evidence: NAS reference: PMID:9244297 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS from a study describing the Fu/Cos2/Ci complex. review_file: genes/DROME/fu/fu-ai-review.yaml - organism: ECOLI gene: fliI qualifier: involved_in term: id: GO:0006935 label: chemotaxis evidence: NAS reference: PMID:31337100 review_action: MARK_AS_OVER_ANNOTATED review_summary: This NAS row comes from a general review of flagellar motility. FliI is a flagellar export ATPase needed to build the flagellum. It has no role in chemoreception, signal transduction or motor switching. Chemotaxis fails in fliI mutants only because no flagella are made. review_file: genes/ECOLI/fliI/fliI-ai-review.yaml - organism: SCHPO gene: gaa1 qualifier: involved_in term: id: GO:0031505 label: fungal-type cell wall organization evidence: NAS reference: PMID:15003443 review_action: MARK_AS_OVER_ANNOTATED review_summary: While GPI-anchored proteins contribute to cell wall organization in fungi, this is an indirect downstream effect. The direct function of gaa1 is GPI anchor attachment, not cell wall organization itself; this annotation overshoots the gene's direct role and is marked as over-annotated. review_file: genes/SCHPO/gaa1/gaa1-ai-review.yaml - organism: human gene: ADRM1 qualifier: involved_in term: id: GO:0006979 label: response to oxidative stress evidence: NAS reference: PMID:35858375 review_action: MARK_AS_OVER_ANNOTATED review_summary: The cited PA28-20S structural work does not provide ADRM1-specific oxidative-stress function. review_file: genes/human/ADRM1/ADRM1-ai-review.yaml - organism: human gene: ADRM1 qualifier: located_in term: id: GO:0008021 label: synaptic vesicle evidence: NAS reference: PMID:37228199 review_action: MARK_AS_OVER_ANNOTATED review_summary: The cited work supports free 19S regulatory particles near synapses, but not ADRM1 as a synaptic-vesicle component. review_file: genes/human/ADRM1/ADRM1-ai-review.yaml - organism: human gene: ADRM1 qualifier: involved_in term: id: GO:0071357 label: cellular response to type I interferon evidence: NAS reference: PMID:31380390 review_action: MARK_AS_OVER_ANNOTATED review_summary: The cited review discusses proteasome regulation in broad cellular contexts and does not establish ADRM1 as a direct type-I-interferon response effector. review_file: genes/human/ADRM1/ADRM1-ai-review.yaml - organism: human gene: AEBP2 qualifier: involved_in term: id: GO:0031507 label: heterochromatin formation evidence: NAS reference: PMID:33514705 review_action: MARK_AS_OVER_ANNOTATED review_summary: Over-annotated for this protein. The term reaches AEBP2 only as a ComplexPortal projection of a complex-level property, the cited reference performs no assay of heterochromatin assembly, and what AEBP2-specific functional data exist point the other way for the isoform that human tissues actually express. review_file: genes/human/AEBP2/AEBP2-ai-review.yaml - organism: human gene: AEBP2 qualifier: involved_in term: id: GO:0031507 label: heterochromatin formation evidence: NAS reference: PMID:29348366 review_action: MARK_AS_OVER_ANNOTATED review_summary: The same complex-level projection from the companion structural paper, and equally over-annotated for AEBP2. review_file: genes/human/AEBP2/AEBP2-ai-review.yaml - organism: human gene: AGO3 qualifier: involved_in term: id: GO:0035196 label: miRNA processing evidence: NAS reference: PMID:28781232 review_action: MARK_AS_OVER_ANNOTATED review_summary: miRNA processing overstates the direct role of AGO3 in canonical miRNA biogenesis. review_file: genes/human/AGO3/AGO3-ai-review.yaml - organism: human gene: AHNAK qualifier: involved_in term: id: GO:1905686 label: positive regulation of plasma membrane repair evidence: NAS reference: PMID:22940583 review_action: MARK_AS_OVER_ANNOTATED review_summary: Positive regulation of plasma membrane repair. The cited paper contains no membrane-repair experiment, and the one experiment that tested AHNAK in membrane repair found no requirement. review_file: genes/human/AHNAK/AHNAK-ai-review.yaml - organism: human gene: AMN qualifier: part_of term: id: GO:0043235 label: signaling receptor complex evidence: IPI reference: PMID:30523278 review_action: MARK_AS_OVER_ANNOTATED review_summary: Records AMN's membership in the cubam receptor complex via its structurally resolved interaction with cubilin. However, cubam is an endocytic/cargo receptor, not a signaling receptor; the "signaling" qualifier is an over-annotation. review_file: genes/human/AMN/AMN-ai-review.yaml - organism: human gene: AP1S2 qualifier: involved_in term: id: GO:0060155 label: platelet dense granule organization evidence: NAS reference: PMID:23247405 review_action: MARK_AS_OVER_ANNOTATED review_summary: ComplexPortal projection of a speculative sentence. The cited commentary contains no platelet experiment, no AP-1 platelet experiment, and no sigma-isoform resolution; its only platelet statement is an explicit prediction about Rab38. review_file: genes/human/AP1S2/AP1S2-ai-review.yaml - organism: human gene: AP1S2 qualifier: involved_in term: id: GO:1903232 label: melanosome assembly evidence: NAS reference: PMID:23247405 review_action: MARK_AS_OVER_ANNOTATED review_summary: Melanosome assembly, projected from the same commentary. AP-1 involvement in melanosomal cargo traffic is real, but the experiments used pan-AP-1 reagents in melanocytes and say nothing about which sigma isoform is present. review_file: genes/human/AP1S2/AP1S2-ai-review.yaml - organism: human gene: ASPSCR1 qualifier: involved_in term: id: GO:0036503 label: ERAD quality control pathway evidence: NAS reference: PMID:36656859 review_action: MARK_AS_OVER_ANNOTATED review_summary: ERAD quality control pathway (NAS). ASPSCR1 regulates p97, which drives ERAD, but overproduction of ASPSCR1 disrupts p97 hexamer function in ERAD. Its role is to modulate p97 assembly rather than to carry out ERAD, and the NAS statement overstates participation. Marked as over-annotated. review_file: genes/human/ASPSCR1/ASPSCR1-ai-review.yaml - organism: human gene: ATF3 qualifier: part_of term: id: GO:0090575 label: RNA polymerase II transcription regulator complex evidence: IPI reference: PMID:20102225 review_action: MARK_AS_OVER_ANNOTATED review_summary: ComplexPortal-derived part_of annotation citing a high-throughput bZIP interaction screen; ATF3 dimerization is real but this row is downstream of a generic PPI dataset and does not specifically demonstrate stable transcription-regulator-complex assembly. review_file: genes/human/ATF3/ATF3-ai-review.yaml - organism: human gene: ATF3 qualifier: part_of term: id: GO:0090575 label: RNA polymerase II transcription regulator complex evidence: IPI reference: PMID:23661758 review_action: MARK_AS_OVER_ANNOTATED review_summary: ComplexPortal-derived part_of annotation citing a high-throughput bZIP interaction network; the underlying screen tests pairwise bZIP dimerization rather than complex assembly with the broader Pol II transcription machinery. review_file: genes/human/ATF3/ATF3-ai-review.yaml - organism: human gene: ATG13 qualifier: part_of term: id: GO:0035032 label: phosphatidylinositol 3-kinase complex, class III evidence: IPI reference: PMID:40442316 review_action: MARK_AS_OVER_ANNOTATED review_summary: ULK1C (including ATG13) and PI3KC3-C1 coassemble into a supercomplex in vitro. review_file: genes/human/ATG13/ATG13-ai-review.yaml - organism: human gene: ATG13 qualifier: involved_in term: id: GO:1903059 label: regulation of protein lipidation evidence: IDA reference: PMID:19225151 review_action: MARK_AS_OVER_ANNOTATED review_summary: In the cited study ATG13 knockdown inhibited autophagosome formation but the authors conclude ATG13 may not be essential for LC3 lipidation. review_file: genes/human/ATG13/ATG13-ai-review.yaml - organism: human gene: ATP6V0A1 qualifier: located_in term: id: GO:0016020 label: membrane evidence: IDA reference: PMID:33065002 review_action: MARK_AS_OVER_ANNOTATED review_summary: Correct but too broad. ATP6V0A1 is a membrane protein, but generic membrane does not capture its V0-sector/endolysosomal and vesicular membrane identity. review_file: genes/human/ATP6V0A1/ATP6V0A1-ai-review.yaml - organism: human gene: ATP6V1A qualifier: located_in term: id: GO:0016020 label: membrane evidence: IDA reference: PMID:33065002 review_action: MARK_AS_OVER_ANNOTATED review_summary: Generic membrane annotation from the cryo-EM structure paper. Too generic relative to the more specific lysosomal membrane and endosome membrane annotations. review_file: genes/human/ATP6V1A/ATP6V1A-ai-review.yaml - organism: human gene: ATP6V1D qualifier: located_in term: id: GO:0016020 label: membrane evidence: IDA reference: PMID:33065002 review_action: MARK_AS_OVER_ANNOTATED review_summary: IDA from the human V-ATPase structural study (cryo-EM). The D subunit is part of the membrane-associated V-ATPase complex on the cytoplasmic face of membranes. review_file: genes/human/ATP6V1D/ATP6V1D-ai-review.yaml - organism: human gene: ATP6V1D qualifier: involved_in term: id: GO:0051452 label: intracellular pH reduction evidence: NAS reference: PMID:32001091 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS from V-ATPase review. Intracellular pH reduction is a core outcome of V-ATPase activity. This term is somewhat redundant with the more specific acidification terms. review_file: genes/human/ATP6V1D/ATP6V1D-ai-review.yaml - organism: human gene: ATP6V1F qualifier: located_in term: id: GO:0016020 label: membrane evidence: IDA reference: PMID:33065002 review_action: MARK_AS_OVER_ANNOTATED review_summary: IDA from the cryo-EM study. F subunit is associated with membrane as part of the V-ATPase complex. review_file: genes/human/ATP6V1F/ATP6V1F-ai-review.yaml - organism: human gene: ATP6V1F qualifier: involved_in term: id: GO:0051452 label: intracellular pH reduction evidence: NAS reference: PMID:32001091 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS from V-ATPase review. Generic term for the acidification function. review_file: genes/human/ATP6V1F/ATP6V1F-ai-review.yaml - organism: human gene: ATXN7 qualifier: involved_in term: id: GO:0006282 label: regulation of DNA repair evidence: NAS reference: PMID:11406595 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Regulation of DNA repair (NAS). Principle used here: NAS complex rows that state membership or coactivator function are accepted, because they hold for every subunit; rows asserting a side activity of the complex are not. The source papers describe activities of the TFTC/STAGA complexes (a link to UV-damaged-DNA recognition, a connection to splicing factors) before ATXN7 was identified as a subunit. They do not test ATXN7, and the complex-level observation does not establish that ATXN7 takes part in this process. Over-annotation.' review_file: genes/human/ATXN7/ATXN7-ai-review.yaml - organism: human gene: ATXN7 qualifier: involved_in term: id: GO:0006282 label: regulation of DNA repair evidence: NAS reference: PMID:11564863 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Regulation of DNA repair (NAS). Principle used here: NAS complex rows that state membership or coactivator function are accepted, because they hold for every subunit; rows asserting a side activity of the complex are not. The source papers describe activities of the TFTC/STAGA complexes (a link to UV-damaged-DNA recognition, a connection to splicing factors) before ATXN7 was identified as a subunit. They do not test ATXN7, and the complex-level observation does not establish that ATXN7 takes part in this process. Over-annotation.' review_file: genes/human/ATXN7/ATXN7-ai-review.yaml - organism: human gene: ATXN7 qualifier: involved_in term: id: GO:0043484 label: regulation of RNA splicing evidence: NAS reference: PMID:11564863 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Regulation of RNA splicing (NAS). Principle used here: NAS complex rows that state membership or coactivator function are accepted, because they hold for every subunit; rows asserting a side activity of the complex are not. The source papers describe activities of the TFTC/STAGA complexes (a link to UV-damaged-DNA recognition, a connection to splicing factors) before ATXN7 was identified as a subunit. They do not test ATXN7, and the complex-level observation does not establish that ATXN7 takes part in this process. Over-annotation.' review_file: genes/human/ATXN7/ATXN7-ai-review.yaml - organism: human gene: AUTS2 qualifier: involved_in term: id: GO:0031507 label: heterochromatin formation evidence: NAS reference: PMID:22325352 review_action: MARK_AS_OVER_ANNOTATED review_summary: General PRC1 compaction should not be assigned uniformly to AUTS2. review_file: genes/human/AUTS2/AUTS2-ai-review.yaml - organism: human gene: BABAM1 qualifier: involved_in term: id: GO:0034516 label: response to vitamin B6 evidence: NAS reference: PMID:31142841 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Response to vitamin B6 (NAS). The source shows that intracellular pyridoxal-5''-phosphate controls whether the metabolic enzyme SHMT2 binds and inhibits BRISC: only PLP-free SHMT2 dimers bind. The vitamin B6 sensing is done by SHMT2, and BABAM1 is a structural BRISC subunit downstream of it. Over-annotation.' review_file: genes/human/BABAM1/BABAM1-ai-review.yaml - organism: human gene: BABAM2 qualifier: involved_in term: id: GO:0034516 label: response to vitamin B6 evidence: NAS reference: PMID:31142841 review_action: MARK_AS_OVER_ANNOTATED review_summary: Response to vitamin B6 (NAS). PLP is sensed by SHMT2, which binds and inhibits BRISC only as a PLP-free dimer. BABAM2 is a structural BRISC subunit downstream of that sensing. Over-annotation. review_file: genes/human/BABAM2/BABAM2-ai-review.yaml - organism: human gene: BCOR qualifier: involved_in term: id: GO:0031507 label: heterochromatin formation evidence: NAS reference: PMID:22325352 review_action: MARK_AS_OVER_ANNOTATED review_summary: The source supports PRC1-family repression more directly than BCOR-specific heterochromatin formation. review_file: genes/human/BCOR/BCOR-ai-review.yaml - organism: human gene: CDK13 qualifier: involved_in term: id: GO:0009966 label: regulation of signal transduction evidence: IDA reference: PMID:26748711 review_action: MARK_AS_OVER_ANNOTATED review_summary: Signaling-category enrichment extends beyond the measured transcriptional response. review_file: genes/human/CDK13/CDK13-ai-review.yaml - organism: human gene: CHMP4C qualifier: involved_in term: id: GO:0039702 label: viral budding via host ESCRT complex evidence: IDA reference: PMID:24878737 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Likely paralog over-annotation for CHMP4C viral budding context: viral budding via host ESCRT complex.' review_file: genes/human/CHMP4C/CHMP4C-ai-review.yaml - organism: human gene: CHMP4C qualifier: involved_in term: id: GO:0046761 label: viral budding from plasma membrane evidence: IDA reference: PMID:24878737 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Likely paralog over-annotation for CHMP4C viral budding context: viral budding from plasma membrane.' review_file: genes/human/CHMP4C/CHMP4C-ai-review.yaml - organism: human gene: CHMP5 qualifier: involved_in term: id: GO:0039702 label: viral budding via host ESCRT complex evidence: IDA reference: PMID:24878737 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Viral budding is not a core CHMP5 cellular function and is likely over-annotated here: viral budding via host ESCRT complex.' review_file: genes/human/CHMP5/CHMP5-ai-review.yaml - organism: human gene: CHMP5 qualifier: involved_in term: id: GO:0046761 label: viral budding from plasma membrane evidence: IDA reference: PMID:24878737 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Viral budding is not a core CHMP5 cellular function and is likely over-annotated here: viral budding from plasma membrane.' review_file: genes/human/CHMP5/CHMP5-ai-review.yaml - organism: human gene: CHMP6 qualifier: involved_in term: id: GO:0039702 label: viral budding via host ESCRT complex evidence: IDA reference: PMID:24878737 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Over-annotated CHMP6 viral-budding term: viral budding via host ESCRT complex.' review_file: genes/human/CHMP6/CHMP6-ai-review.yaml - organism: human gene: CHMP6 qualifier: involved_in term: id: GO:0046761 label: viral budding from plasma membrane evidence: IDA reference: PMID:24878737 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Over-annotated CHMP6 viral-budding term: viral budding from plasma membrane.' review_file: genes/human/CHMP6/CHMP6-ai-review.yaml - organism: human gene: CHMP7 qualifier: located_in term: id: GO:0005886 label: plasma membrane evidence: IDA reference: PMID:24878737 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Plasma-membrane location/context is over-extended for CHMP7: plasma membrane.' review_file: genes/human/CHMP7/CHMP7-ai-review.yaml - organism: human gene: CHMP7 qualifier: involved_in term: id: GO:0039702 label: viral budding via host ESCRT complex evidence: IDA reference: PMID:24878737 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Over-annotated CHMP7 viral-budding term: viral budding via host ESCRT complex.' review_file: genes/human/CHMP7/CHMP7-ai-review.yaml - organism: human gene: CHMP7 qualifier: involved_in term: id: GO:0046761 label: viral budding from plasma membrane evidence: IDA reference: PMID:24878737 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'Over-annotated CHMP7 viral-budding term: viral budding from plasma membrane.' review_file: genes/human/CHMP7/CHMP7-ai-review.yaml - organism: human gene: CSNK2B qualifier: involved_in term: id: GO:0031507 label: heterochromatin formation evidence: NAS reference: PMID:22325352 review_action: MARK_AS_OVER_ANNOTATED review_summary: Heterochromatin formation assigned via CSNK2B co-membership in PRC1-family complexes. This is a process transfer from the broader Polycomb complex; CSNK2B's direct contribution is its kinase-regulatory role within embedded CK2, not chromatin compaction per se. review_file: genes/human/CSNK2B/CSNK2B-ai-review.yaml - organism: human gene: CUL1 qualifier: involved_in term: id: GO:0006355 label: regulation of DNA-templated transcription evidence: NAS reference: PMID:36372232 review_action: MARK_AS_OVER_ANNOTATED review_summary: SCF(FBXL14) ubiquitinates the Pol I catalytic subunit RPA194 under transcription stress. review_file: genes/human/CUL1/CUL1-ai-review.yaml - organism: human gene: CUL1 qualifier: involved_in term: id: GO:0014033 label: neural crest cell differentiation evidence: NAS reference: PMID:30190310 review_action: MARK_AS_OVER_ANNOTATED review_summary: SCF(FBXL17) dimerization quality control is required for neural crest and neuronal differentiation. review_file: genes/human/CUL1/CUL1-ai-review.yaml - organism: human gene: CUL1 qualifier: involved_in term: id: GO:0042981 label: regulation of apoptotic process evidence: NAS reference: PMID:25654763 review_action: MARK_AS_OVER_ANNOTATED review_summary: SCF(FBXL18) degrades the pro-apoptotic F-box protein FBXL7. review_file: genes/human/CUL1/CUL1-ai-review.yaml - organism: human gene: CUL1 qualifier: involved_in term: id: GO:0060173 label: limb development evidence: NAS reference: PMID:10471509 review_action: MARK_AS_OVER_ANNOTATED review_summary: The mouse dactylaplasia locus encodes the F-box/WD40 protein dactylin (Fbxw4). review_file: genes/human/CUL1/CUL1-ai-review.yaml - organism: human gene: DCAF11 qualifier: involved_in term: id: GO:1902412 label: regulation of mitotic cytokinesis evidence: NAS reference: PMID:34758320 review_action: MARK_AS_OVER_ANNOTATED review_summary: The cited paper shows DCAF11 mediates phospho-Ser68 CENP-A degradation to maintain centromere identity and prevent ectopic CENP-A localization during the cell cycle; it does not demonstrate a role in cytokinesis. This label over-reaches the evidence. review_file: genes/human/DCAF11/DCAF11-ai-review.yaml - organism: human gene: DPM2 qualifier: involved_in term: id: GO:0043048 label: dolichyl monophosphate biosynthetic process evidence: IDA reference: PMID:10835346 review_action: MARK_AS_OVER_ANNOTATED review_summary: IDA annotation to "dolichyl monophosphate biosynthetic process". PMID:10835346 concerns dolichol-phosphate-MANNOSE (Dol-P-Man) synthesis, i.e. the transfer of mannose onto dolichyl phosphate, rather than the biosynthesis of dolichyl monophosphate itself. The chosen term is therefore an imprecise/misleading match for the underlying experiment. review_file: genes/human/DPM2/DPM2-ai-review.yaml - organism: human gene: DYNC1H1 qualifier: located_in term: id: GO:0001673 label: male germ cell nucleus evidence: NAS reference: PMID:36973253 review_action: MARK_AS_OVER_ANNOTATED review_summary: Male germ cell nucleus (NAS) from a mouse DYNLRB2 meiosis paper; the paper places DYNC1H1 at spindle poles of spermatocytes, not in the nucleus. review_file: genes/human/DYNC1H1/DYNC1H1-ai-review.yaml - organism: human gene: FBXO43 qualifier: part_of term: id: GO:0019005 label: SCF ubiquitin ligase complex evidence: NAS reference: PMID:34445249 review_action: MARK_AS_OVER_ANNOTATED review_summary: ComplexPortal author-statement assigning FBXO43 to an SCF ubiquitin ligase complex based on its F-box. However, UniProt records that FBXO43 does not interact with SKP1 (PMID:34595750), and FBXO43 instead binds directly to APC/C subunits. review_file: genes/human/FBXO43/FBXO43-ai-review.yaml - organism: human gene: FBXO43 qualifier: involved_in term: id: GO:0031146 label: SCF-dependent proteasomal ubiquitin-dependent protein catabolic process evidence: NAS reference: PMID:34445249 review_action: MARK_AS_OVER_ANNOTATED review_summary: ComplexPortal author-statement assigning FBXO43 to SCF-dependent proteasomal protein catabolism. FBXO43 is itself degraded by the ubiquitin-proteasome system after calcium-triggered phosphorylation; no productive SCF substrate-receptor role is established and SKP1 interaction is reported not to occur. review_file: genes/human/FBXO43/FBXO43-ai-review.yaml - organism: human gene: FBXO5 qualifier: involved_in term: id: GO:0031146 label: SCF-dependent proteasomal ubiquitin-dependent protein catabolic process evidence: NAS reference: PMID:34445249 review_action: MARK_AS_OVER_ANNOTATED review_summary: ComplexPortal author-statement assigning EMI1 to SCF-dependent proteasomal protein catabolism. EMI1 is a substrate (degraded by SCF-beta-TrCP) rather than a demonstrated substrate-receptor driving degradation of other proteins via SCF. review_file: genes/human/FBXO5/FBXO5-ai-review.yaml - organism: human gene: GLRX5 qualifier: involved_in term: id: GO:0045454 label: cell redox homeostasis evidence: NAS reference: PMID:27532772 review_action: MARK_AS_OVER_ANNOTATED review_summary: While glutaredoxins are generally involved in redox homeostasis, GLRX5 is a specialized monothiol glutaredoxin whose primary function is iron-sulfur cluster transfer rather than general redox chemistry. review_file: genes/human/GLRX5/GLRX5-ai-review.yaml - organism: human gene: H3C2 qualifier: located_in term: id: GO:0070062 label: extracellular exosome evidence: IPI reference: PMID:37384673 review_action: MARK_AS_OVER_ANNOTATED review_summary: Extracellular exosome (IPI, ComplexPortal) attached to the nucleosome complex citing a cryo-EM study of the INO80-hexasome complex. review_file: genes/human/H3C2/H3C2-ai-review.yaml - organism: human gene: HRAS qualifier: involved_in term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence: IDA reference: PMID:23027131 review_action: MARK_AS_OVER_ANNOTATED review_summary: This transcription annotation is based on a downstream oncogenic Ras model and should not be treated as a direct HRAS function. review_file: genes/human/HRAS/HRAS-ai-review.yaml - organism: human gene: IL21 qualifier: located_in term: id: GO:0005886 label: plasma membrane evidence: IPI reference: PMID:37339051 review_action: MARK_AS_OVER_ANNOTATED review_summary: This annotation likely refers to IL21 associating with plasma membrane via receptor binding (IL21R is membrane-bound). However, IL21 itself is a secreted protein, not a membrane protein. This may be misleading - IL21 is transiently at the membrane when bound to receptor but its primary location is extracellular. review_file: genes/human/IL21/IL21-ai-review.yaml - organism: human gene: IL21 qualifier: involved_in term: id: GO:0016064 label: immunoglobulin mediated immune response evidence: NAS reference: PMID:37339051 review_action: MARK_AS_OVER_ANNOTATED review_summary: IL21 promotes immunoglobulin production by B cells, thus indirectly supporting immunoglobulin-mediated immunity. However, IL21 itself does not directly participate in immunoglobulin-mediated immune responses - it's an upstream regulator. review_file: genes/human/IL21/IL21-ai-review.yaml - organism: human gene: KRAS qualifier: part_of term: id: GO:0000164 label: protein phosphatase type 1 complex evidence: IPI reference: PMID:36175670 review_action: MARK_AS_OVER_ANNOTATED review_summary: SHOC2-MRAS-PP1C studies show that canonical RAS proteins, including KRAS, can bind this regulatory phosphatase system with lower affinity than MRAS. review_file: genes/human/KRAS/KRAS-ai-review.yaml - organism: human gene: KRAS qualifier: involved_in term: id: GO:0043069 label: negative regulation of programmed cell death evidence: NAS reference: PMID:39788953 review_action: MARK_AS_OVER_ANNOTATED review_summary: Negative regulation of programmed cell death can occur downstream of RAS effector pathways, especially through PI3K-AKT survival signaling, but the annotation is broad. review_file: genes/human/KRAS/KRAS-ai-review.yaml - organism: human gene: KRAS qualifier: part_of term: id: GO:1902554 label: serine/threonine protein kinase complex evidence: IPI reference: PMID:33608534 review_action: MARK_AS_OVER_ANNOTATED review_summary: The cited RAF1 structural work supports KRAS binding to RAF regulatory domains during RAF activation, not stable membership in a serine/threonine protein kinase complex. review_file: genes/human/KRAS/KRAS-ai-review.yaml - organism: human gene: KRAS qualifier: part_of term: id: GO:1905360 label: GTPase complex evidence: IPI reference: PMID:39043660 review_action: MARK_AS_OVER_ANNOTATED review_summary: The GTPase complex annotation is based on a structural interaction context rather than evidence that KRAS is a stable component of a native cellular complex. review_file: genes/human/KRAS/KRAS-ai-review.yaml - organism: human gene: LPL qualifier: part_of term: id: GO:1902494 label: catalytic complex evidence: IPI reference: PMID:30559189 review_action: MARK_AS_OVER_ANNOTATED review_summary: The generic catalytic-complex annotation is too vague to identify an LPL assembly. review_file: genes/human/LPL/LPL-ai-review.yaml - organism: human gene: NDUFA10 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS (ComplexPortal) annotation linking Complex I to proton-motive-force-driven ATP synthesis. This is downstream of Complex I proton pumping (performed by the core subunits), not a function of the accessory subunit NDUFA10 itself. review_file: genes/human/NDUFA10/NDUFA10-ai-review.yaml - organism: human gene: NDUFA13 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: Complex-level BP (NAS, ComplexPortal). Complex I contributes to the proton gradient that drives ATP synthesis, but ATP synthesis itself is performed by Complex V, and NDUFA13 is a non-catalytic accessory subunit. This is an over-annotation at the level of the individual subunit. review_file: genes/human/NDUFA13/NDUFA13-ai-review.yaml - organism: human gene: NDUFA2 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: ATP synthesis is performed by Complex V, and the proton-motive force is generated by the coupled respiratory chain complexes as a whole. A non-catalytic accessory subunit of Complex I does not participate in ATP synthesis in any specific way; this is a distal pathway-level term and is an over-annotation for NDUFA2. review_file: genes/human/NDUFA2/NDUFA2-ai-review.yaml - organism: human gene: NDUFA5 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: Annotation to proton motive force-driven ATP synthesis. This process is executed by ATP synthase (Complex V); Complex I contributes only indirectly by helping generate the proton gradient. Attributing ATP synthesis to the matrix-arm accessory subunit NDUFA5 over-reaches. review_file: genes/human/NDUFA5/NDUFA5-ai-review.yaml - organism: human gene: NDUFA6 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: ATP synthesis is carried out by Complex V, not Complex I. Complex I contributes upstream by generating the proton-motive force, and NDUFA6 contributes only as a structural subunit of Complex I. This term is well removed from NDUFA6's direct function and represents a system-level over-attribution rather than the gene's specific role. review_file: genes/human/NDUFA6/NDUFA6-ai-review.yaml - organism: human gene: NDUFA8 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS (ComplexPortal) involvement in proton-motive-force-driven ATP synthesis. ATP synthesis is carried out by Complex V (ATP synthase); Complex I contributes only by helping generate the proton gradient, and NDUFA8 is a non-catalytic subunit of Complex I. This is a downstream, complex/pathway-level process incorrectly ascribed to the individual subunit's function; over-annotation for NDUFA8. review_file: genes/human/NDUFA8/NDUFA8-ai-review.yaml - organism: human gene: NDUFA9 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS (ComplexPortal) annotation to proton motive force-driven mitochondrial ATP synthesis. Complex I generates part of the proton-motive force that drives ATP synthase, but ATP synthesis is performed by Complex V; NDUFA9 as a non-catalytic accessory subunit contributes only indirectly and distally to this process. This is an over-broad process for a structural subunit. review_file: genes/human/NDUFA9/NDUFA9-ai-review.yaml - organism: human gene: NDUFB10 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: Author statement (ComplexPortal) linking Complex I to proton-motive-force ATP synthesis. This is an OXPHOS system-level / downstream outcome, not a function of this non-catalytic accessory subunit (ATP synthesis is performed by Complex V). Over-attribution of a pathway-level process to a single subunit. review_file: genes/human/NDUFB10/NDUFB10-ai-review.yaml - organism: human gene: NDUFB11 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: Non-traceable author statement (ComplexPortal) linking the OXPHOS system to proton-motive-force-driven ATP synthesis. ATP synthesis is downstream of Complex I and is carried out by Complex V; this is a holoenzyme/pathway-level annotation that over-reaches for an individual Complex I accessory subunit. Marked as over-annotated. review_file: genes/human/NDUFB11/NDUFB11-ai-review.yaml - organism: human gene: NDUFB7 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS annotation (ComplexPortal) to proton-motive-force-driven ATP synthesis. This is the terminal OXPHOS process (Complex V); Complex I contributes to the proton-motive force upstream, but ATP synthesis itself is not a direct process of Complex I or of the non-catalytic subunit NDUFB7. Over-annotation of the individual subunit. review_file: genes/human/NDUFB7/NDUFB7-ai-review.yaml - organism: human gene: NDUFB9 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS (ComplexPortal) annotation to proton-motive-force-driven ATP synthesis. This describes the downstream OXPHOS outcome of the proton gradient; NDUFB9 is a non-catalytic accessory subunit of Complex I and does not itself synthesize ATP or pump protons. This is an over-annotation for an accessory subunit — the proton gradient is generated by the complex, and ATP synthesis is performed by Complex V. review_file: genes/human/NDUFB9/NDUFB9-ai-review.yaml - organism: human gene: NDUFC2 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS (ComplexPortal) involvement in proton-motive-force-driven ATP synthesis. ATP synthesis is carried out by Complex V (ATP synthase); Complex I only contributes upstream to the proton gradient. Assigning the ATP-synthesis process directly to a Complex I accessory subunit conflates distinct complexes and is an over-annotation. review_file: genes/human/NDUFC2/NDUFC2-ai-review.yaml - organism: human gene: NDUFS6 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: Author-stated (NAS, ComplexPortal) involvement in proton motive force-driven ATP synthesis. ATP synthesis is carried out by Complex V (ATP synthase); Complex I only contributes to the proton-motive force. This over-reaches for a matrix-side accessory subunit of Complex I. review_file: genes/human/NDUFS6/NDUFS6-ai-review.yaml - organism: human gene: NDUFS7 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: Complex I contributes to the proton motive force that drives ATP synthase, but it is not itself part of the ATP-synthesis reaction. review_file: genes/human/NDUFS7/NDUFS7-ai-review.yaml - organism: human gene: NDUFS8 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: ComplexPortal NAS annotation linking Complex I to proton-motive-force-driven ATP synthesis. Complex I contributes to the proton-motive force, but ATP synthesis is carried out by Complex V; for NDUFS8 this is a downstream pathway-level role. review_file: genes/human/NDUFS8/NDUFS8-ai-review.yaml - organism: human gene: NDUFV2 qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: Author-statement (NAS, ComplexPortal) annotation to proton motive force-driven ATP synthesis. ATP synthesis is the function of Complex V (ATP synthase); Complex I contributes only indirectly by helping establish the proton-motive force via its membrane arm, and NDUFV2 (an N-module electron-input subunit) is doubly removed from ATP synthesis. review_file: genes/human/NDUFV2/NDUFV2-ai-review.yaml - organism: human gene: PAM16 qualifier: involved_in term: id: GO:0006886 label: intracellular protein transport evidence: NAS reference: PMID:10339406 review_action: MARK_AS_OVER_ANNOTATED review_summary: Correct pathway family but too broad. PAM16 specifically supports TIM23/PAM-mediated mitochondrial matrix protein import. review_file: genes/human/PAM16/PAM16-ai-review.yaml - organism: human gene: PANK3 qualifier: located_in term: id: GO:0005634 label: nucleus evidence: IPI reference: PMID:17631502 review_action: MARK_AS_OVER_ANNOTATED review_summary: Nuclear location assigned by ComplexPortal (IPI). PMID:17631502 is a crystal structure paper on the PanK3 catalytic core in complex with acetyl-CoA and does not localize PANK3 to the nucleus. Direct live-cell imaging (PMID:23152917) shows human PanK3 is cytosolic. Nuclear location is a property of PanK1alpha, not PanK3, so this is an over-annotation. Per policy this experimental (IPI) annotation is flagged as over-annotated rather than removed. review_file: genes/human/PANK3/PANK3-ai-review.yaml - organism: human gene: PMPCA qualifier: involved_in term: id: GO:0070585 label: protein localization to mitochondrion evidence: NAS reference: PMID:32443488 review_action: MARK_AS_OVER_ANNOTATED review_summary: MPP processing is coupled to import for some substrates, but PMPCA acts after import by cleaving targeting presequences rather than serving as the localization/import machinery. review_file: genes/human/PMPCA/PMPCA-ai-review.yaml - organism: human gene: PMPCB qualifier: located_in term: id: GO:0005739 label: mitochondrion evidence: NAS reference: PMID:32443488 review_action: MARK_AS_OVER_ANNOTATED review_summary: Correct but broad. PMPCB is specifically a mitochondrial matrix MPP complex subunit. review_file: genes/human/PMPCB/PMPCB-ai-review.yaml - organism: human gene: PMPCB qualifier: involved_in term: id: GO:0070585 label: protein localization to mitochondrion evidence: NAS reference: PMID:32443488 review_action: MARK_AS_OVER_ANNOTATED review_summary: Over-annotated. PMPCB acts after protein import by cleaving targeting presequences; it is not itself the import/localization machinery. review_file: genes/human/PMPCB/PMPCB-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0002376 label: immune system process evidence: NAS reference: PMID:33019542 review_action: MARK_AS_OVER_ANNOTATED review_summary: immune system process is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0006281 label: DNA repair evidence: NAS reference: PMID:32134919 review_action: MARK_AS_OVER_ANNOTATED review_summary: DNA repair is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0006915 label: apoptotic process evidence: NAS reference: PMID:32935661 review_action: MARK_AS_OVER_ANNOTATED review_summary: apoptotic process is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0006974 label: DNA damage response evidence: NAS reference: PMID:32134919 review_action: MARK_AS_OVER_ANNOTATED review_summary: DNA damage response is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0006979 label: response to oxidative stress evidence: IDA reference: PMID:34702852 review_action: MARK_AS_OVER_ANNOTATED review_summary: response to oxidative stress is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0006979 label: response to oxidative stress evidence: NAS reference: PMID:35858375 review_action: MARK_AS_OVER_ANNOTATED review_summary: response to oxidative stress is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0007283 label: spermatogenesis evidence: NAS reference: PMID:23706739 review_action: MARK_AS_OVER_ANNOTATED review_summary: spermatogenesis is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0030317 label: flagellated sperm motility evidence: NAS reference: PMID:23706739 review_action: MARK_AS_OVER_ANNOTATED review_summary: flagellated sperm motility is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0030317 label: flagellated sperm motility evidence: NAS reference: PMID:27003159 review_action: MARK_AS_OVER_ANNOTATED review_summary: flagellated sperm motility is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0032729 label: positive regulation of type II interferon production evidence: NAS reference: PMID:30104634 review_action: MARK_AS_OVER_ANNOTATED review_summary: positive regulation of type II interferon production is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0032743 label: positive regulation of interleukin-2 production evidence: NAS reference: PMID:30104634 review_action: MARK_AS_OVER_ANNOTATED review_summary: positive regulation of interleukin-2 production is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0032760 label: positive regulation of tumor necrosis factor production evidence: NAS reference: PMID:30104634 review_action: MARK_AS_OVER_ANNOTATED review_summary: positive regulation of tumor necrosis factor production is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0034341 label: response to type II interferon evidence: NAS reference: PMID:30104634 review_action: MARK_AS_OVER_ANNOTATED review_summary: response to type II interferon is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0043374 label: CD8-positive, alpha-beta T cell differentiation evidence: NAS reference: PMID:33019542 review_action: MARK_AS_OVER_ANNOTATED review_summary: CD8-positive, alpha-beta T cell differentiation is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0045061 label: thymic T cell selection evidence: NAS reference: PMID:30650357 review_action: MARK_AS_OVER_ANNOTATED review_summary: thymic T cell selection is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0045063 label: T-helper 1 cell differentiation evidence: NAS reference: PMID:30104634 review_action: MARK_AS_OVER_ANNOTATED review_summary: T-helper 1 cell differentiation is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0045590 label: negative regulation of regulatory T cell differentiation evidence: NAS reference: PMID:30104634 review_action: MARK_AS_OVER_ANNOTATED review_summary: negative regulation of regulatory T cell differentiation is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0051321 label: meiotic cell cycle evidence: NAS reference: PMID:23706739 review_action: MARK_AS_OVER_ANNOTATED review_summary: meiotic cell cycle is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0061136 label: regulation of proteasomal protein catabolic process evidence: NAS reference: PMID:12032076 review_action: MARK_AS_OVER_ANNOTATED review_summary: regulation of proteasomal protein catabolic process is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0061136 label: regulation of proteasomal protein catabolic process evidence: IDA reference: PMID:35714770 review_action: MARK_AS_OVER_ANNOTATED review_summary: regulation of proteasomal protein catabolic process is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0061136 label: regulation of proteasomal protein catabolic process evidence: NAS reference: PMID:35714770 review_action: MARK_AS_OVER_ANNOTATED review_summary: regulation of proteasomal protein catabolic process is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0071357 label: cellular response to type I interferon evidence: NAS reference: PMID:31380390 review_action: MARK_AS_OVER_ANNOTATED review_summary: cellular response to type I interferon is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0072539 label: T-helper 17 cell differentiation evidence: NAS reference: PMID:30104634 review_action: MARK_AS_OVER_ANNOTATED review_summary: T-helper 17 cell differentiation is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:0160165 label: CD8-positive, alpha-beta T cell homeostasis evidence: NAS reference: PMID:33815406 review_action: MARK_AS_OVER_ANNOTATED review_summary: CD8-positive, alpha-beta T cell homeostasis is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMA1 qualifier: involved_in term: id: GO:2000045 label: regulation of G1/S transition of mitotic cell cycle evidence: NAS reference: PMID:32935661 review_action: MARK_AS_OVER_ANNOTATED review_summary: regulation of G1/S transition of mitotic cell cycle is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMA1. review_file: genes/human/PSMA1/PSMA1-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0006281 label: DNA repair evidence: NAS reference: PMID:32134919 review_action: MARK_AS_OVER_ANNOTATED review_summary: DNA repair is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0006915 label: apoptotic process evidence: NAS reference: PMID:32935661 review_action: MARK_AS_OVER_ANNOTATED review_summary: apoptotic process is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0006974 label: DNA damage response evidence: NAS reference: PMID:32134919 review_action: MARK_AS_OVER_ANNOTATED review_summary: DNA damage response is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0006979 label: response to oxidative stress evidence: IDA reference: PMID:34702852 review_action: MARK_AS_OVER_ANNOTATED review_summary: response to oxidative stress is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0006979 label: response to oxidative stress evidence: NAS reference: PMID:35858375 review_action: MARK_AS_OVER_ANNOTATED review_summary: response to oxidative stress is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0007283 label: spermatogenesis evidence: NAS reference: PMID:23706739 review_action: MARK_AS_OVER_ANNOTATED review_summary: spermatogenesis is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0030317 label: flagellated sperm motility evidence: NAS reference: PMID:23706739 review_action: MARK_AS_OVER_ANNOTATED review_summary: flagellated sperm motility is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0030317 label: flagellated sperm motility evidence: NAS reference: PMID:27003159 review_action: MARK_AS_OVER_ANNOTATED review_summary: flagellated sperm motility is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0051321 label: meiotic cell cycle evidence: NAS reference: PMID:23706739 review_action: MARK_AS_OVER_ANNOTATED review_summary: meiotic cell cycle is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0061136 label: regulation of proteasomal protein catabolic process evidence: NAS reference: PMID:12032076 review_action: MARK_AS_OVER_ANNOTATED review_summary: regulation of proteasomal protein catabolic process is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0061136 label: regulation of proteasomal protein catabolic process evidence: IDA reference: PMID:35714770 review_action: MARK_AS_OVER_ANNOTATED review_summary: regulation of proteasomal protein catabolic process is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0061136 label: regulation of proteasomal protein catabolic process evidence: NAS reference: PMID:35714770 review_action: MARK_AS_OVER_ANNOTATED review_summary: regulation of proteasomal protein catabolic process is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:0071357 label: cellular response to type I interferon evidence: NAS reference: PMID:31380390 review_action: MARK_AS_OVER_ANNOTATED review_summary: cellular response to type I interferon is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: PSMB5 qualifier: involved_in term: id: GO:2000045 label: regulation of G1/S transition of mitotic cell cycle evidence: NAS reference: PMID:32935661 review_action: MARK_AS_OVER_ANNOTATED review_summary: regulation of G1/S transition of mitotic cell cycle is a pathway- or physiology-level consequence of proteasome activity rather than a specific function of PSMB5. review_file: genes/human/PSMB5/PSMB5-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0000122 label: negative regulation of transcription by RNA polymerase II evidence: NAS reference: PMID:28591624 review_action: MARK_AS_OVER_ANNOTATED review_summary: Author statement from the CRL2(VHL) crystal-structure paper. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0006355 label: regulation of DNA-templated transcription evidence: NAS reference: PMID:36372232 review_action: MARK_AS_OVER_ANNOTATED review_summary: SCF(FBXL14) containing RBX1 degrades the Pol I catalytic subunit RPA194 under transcription stress. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0007346 label: regulation of mitotic cell cycle evidence: NAS reference: PMID:36395886 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS row from the SCF(FBXW7)-WDR5 study of mitotic slippage. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0008283 label: cell population proliferation evidence: NAS reference: PMID:30945288 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS row from a CRL4(DCAF4) study in colitis-associated cancer. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0010564 label: regulation of cell cycle process evidence: NAS reference: PMID:31424118 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS rows from reviews and studies of SCF-dependent cell-cycle proteolysis (cyclin F-E2F1, SCF genome stability, ubiquitination in metastasis). review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0010564 label: regulation of cell cycle process evidence: NAS reference: PMID:34445249 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS rows from reviews and studies of SCF-dependent cell-cycle proteolysis (cyclin F-E2F1, SCF genome stability, ubiquitination in metastasis). review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0010564 label: regulation of cell cycle process evidence: NAS reference: PMID:35414786 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS rows from reviews and studies of SCF-dependent cell-cycle proteolysis (cyclin F-E2F1, SCF genome stability, ubiquitination in metastasis). review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0040029 label: epigenetic regulation of gene expression evidence: NAS reference: PMID:30111536 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS rows citing CRL4 ligases that act on chromatin regulators (DNMT1, DNMT3A, SUV39H1, PHGDH). review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0040029 label: epigenetic regulation of gene expression evidence: NAS reference: PMID:34429321 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS rows citing CRL4 ligases that act on chromatin regulators (DNMT1, DNMT3A, SUV39H1, PHGDH). review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0040029 label: epigenetic regulation of gene expression evidence: NAS reference: PMID:34720086 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS rows citing CRL4 ligases that act on chromatin regulators (DNMT1, DNMT3A, SUV39H1, PHGDH). review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0042127 label: regulation of cell population proliferation evidence: NAS reference: PMID:33869224 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS row from a review of Hippo-independent YAP/TAZ regulation. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0042981 label: regulation of apoptotic process evidence: NAS reference: PMID:33898171 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS rows from studies of SCF(FBXL18)/FBXL7 and OTUD1-CRL4(DCAF10)-MCL1 in apoptosis. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0042981 label: regulation of apoptotic process evidence: NAS reference: PMID:25654763 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS rows from studies of SCF(FBXL18)/FBXL7 and OTUD1-CRL4(DCAF10)-MCL1 in apoptosis. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0051726 label: regulation of cell cycle evidence: NAS reference: PMID:33234069 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS row from a review of the FBXL family. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0060173 label: limb development evidence: NAS reference: PMID:10471509 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS row citing the positional cloning of mouse dactylaplasia (Dac/Fbxw4), an F-box/WD40 gene required for maintenance of the apical ectodermal ridge. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:0080135 label: regulation of cellular response to stress evidence: NAS reference: PMID:31586112 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS row from a TFEB/DCAF11-NRF2 study. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:1901524 label: regulation of mitophagy evidence: NAS reference: PMID:36135912 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS row citing a review of mitochondrial fission and fusion, in which FBXL4-containing CRL1 is mentioned. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:1901987 label: regulation of cell cycle phase transition evidence: NAS reference: PMID:16861906 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS rows from CRL4(CDT2) and AMBRA1 studies, where CRL-dependent turnover of licensing and autophagy factors affects phase transitions. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RBX1 qualifier: involved_in term: id: GO:1901987 label: regulation of cell cycle phase transition evidence: NAS reference: PMID:25499913 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS rows from CRL4(CDT2) and AMBRA1 studies, where CRL-dependent turnover of licensing and autophagy factors affects phase transitions. review_file: genes/human/RBX1/RBX1-ai-review.yaml - organism: human gene: RPL18A qualifier: involved_in term: id: GO:0007283 label: spermatogenesis evidence: NAS reference: PMID:36517592 review_action: MARK_AS_OVER_ANNOTATED review_summary: This annotation references a study about male germ-cell-specific ribosomes. While RPL18A is present in ribosomes including those in germ cells, this does not constitute a specific role in spermatogenesis beyond general protein synthesis. The annotation may reflect specialized ribosome composition in germ cells but does not indicate a specific role for RPL18A in spermatogenesis. review_file: genes/human/RPL18A/RPL18A-ai-review.yaml - organism: human gene: RPL36A qualifier: involved_in term: id: GO:0006941 label: striated muscle contraction evidence: NAS reference: PMID:34081545 review_action: MARK_AS_OVER_ANNOTATED review_summary: ComplexPortal propagated striated-muscle contraction from a study that perturbs muscle-specific RPL3L. review_file: genes/human/RPL36A/RPL36A-ai-review.yaml - organism: human gene: RPL36A qualifier: involved_in term: id: GO:1901740 label: negative regulation of myoblast fusion evidence: NAS reference: PMID:26684695 review_action: MARK_AS_OVER_ANNOTATED review_summary: ComplexPortal propagated a myoblast-fusion phenotype from ectopic expression of muscle-specific RPL3L. review_file: genes/human/RPL36A/RPL36A-ai-review.yaml - organism: human gene: RRM2B qualifier: involved_in term: id: GO:0010971 label: positive regulation of G2/M transition of mitotic cell cycle evidence: IDA reference: PMID:10716435 review_action: MARK_AS_OVER_ANNOTATED review_summary: In the founding paper, induction of p53R2 in p53-deficient cells caused G2/M arrest (a checkpoint), not a positive drive through the G2/M transition. RRM2B is a metabolic enzyme; any cell-cycle effect is indirect. review_file: genes/human/RRM2B/RRM2B-ai-review.yaml - organism: human gene: RRM2B qualifier: involved_in term: id: GO:0070318 label: positive regulation of G0 to G1 transition evidence: IDA reference: PMID:11517226 review_action: MARK_AS_OVER_ANNOTATED review_summary: The cited paper shows an R1-p53R2 complex can supply resting (G0/G1) cells with deoxyribonucleotides for DNA repair; it does not demonstrate that RRM2B positively regulates the G0-to-G1 transition. review_file: genes/human/RRM2B/RRM2B-ai-review.yaml - organism: human gene: SDHD qualifier: involved_in term: id: GO:0042776 label: proton motive force-driven mitochondrial ATP synthesis evidence: NAS reference: PMID:30030361 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS annotation from ComplexPortal for proton motive force-driven ATP synthesis. Complex II transfers electrons from succinate to ubiquinone, contributing to the overall electron flow that drives proton pumping by Complexes I, III, and IV, which in turn drives ATP synthesis by Complex V. However, Complex II itself does NOT pump protons. This annotation attributes a downstream consequence of Complex II activity to SDHD rather than a direct function. review_file: genes/human/SDHD/SDHD-ai-review.yaml - organism: human gene: SIRT1 qualifier: involved_in term: id: GO:0042149 label: cellular response to glucose starvation evidence: IMP reference: PMID:18485871 review_action: MARK_AS_OVER_ANNOTATED review_summary: This study links energy status to rRNA transcription, but glucose-specific starvation is not explicit. review_file: genes/human/SIRT1/SIRT1-ai-review.yaml - organism: human gene: SIRT1 qualifier: involved_in term: id: GO:0046015 label: regulation of transcription by glucose evidence: IMP reference: PMID:18485871 review_action: MARK_AS_OVER_ANNOTATED review_summary: The evidence discusses energy status broadly rather than glucose-specific transcriptional control. review_file: genes/human/SIRT1/SIRT1-ai-review.yaml - organism: human gene: SKP1 qualifier: involved_in term: id: GO:0006355 label: regulation of DNA-templated transcription evidence: NAS reference: PMID:36372232 review_action: MARK_AS_OVER_ANNOTATED review_summary: Derived from the identification of SCF(FBXL14) as the E3 that degrades the RNA polymerase I catalytic subunit RPA194 under transcription stress. review_file: genes/human/SKP1/SKP1-ai-review.yaml - organism: human gene: SKP1 qualifier: involved_in term: id: GO:0014033 label: neural crest cell differentiation evidence: NAS reference: PMID:30190310 review_action: MARK_AS_OVER_ANNOTATED review_summary: Derived from the dimerization-quality-control work, in which SCF(FBXL17) clears aberrant BTB dimers and is required for neural crest and neuronal differentiation and survival. review_file: genes/human/SKP1/SKP1-ai-review.yaml - organism: human gene: SKP1 qualifier: involved_in term: id: GO:0031507 label: heterochromatin formation evidence: NAS reference: PMID:22325352 review_action: MARK_AS_OVER_ANNOTATED review_summary: Derived from the PRC1-family proteomics work, via SKP1 membership of the PRC1.1 variant complex. review_file: genes/human/SKP1/SKP1-ai-review.yaml - organism: human gene: SKP1 qualifier: involved_in term: id: GO:0042981 label: regulation of apoptotic process evidence: NAS reference: PMID:25654763 review_action: MARK_AS_OVER_ANNOTATED review_summary: Derived from the FBXL18-FBXL7 study, in which FBXL18 degrades the pro-apoptotic SCF subunit FBXL7 and thereby limits apoptosis. review_file: genes/human/SKP1/SKP1-ai-review.yaml - organism: human gene: SKP1 qualifier: involved_in term: id: GO:0045892 label: negative regulation of DNA-templated transcription evidence: NAS reference: PMID:22325352 review_action: MARK_AS_OVER_ANNOTATED review_summary: Derived from SKP1 membership of PRC1.1/BCOR repressive complexes. review_file: genes/human/SKP1/SKP1-ai-review.yaml - organism: human gene: SKP1 qualifier: involved_in term: id: GO:0060173 label: limb development evidence: NAS reference: PMID:10471509 review_action: MARK_AS_OVER_ANNOTATED review_summary: Derived from the positional cloning of mouse dactylaplasia (Dac), which disrupts an F-box/WD40 gene (FBXW4/dactylin) required for maintenance of the apical ectodermal ridge. review_file: genes/human/SKP1/SKP1-ai-review.yaml - organism: human gene: SLX4 qualifier: involved_in term: id: GO:0006260 label: DNA replication evidence: NAS reference: PMID:34804132 review_action: MARK_AS_OVER_ANNOTATED review_summary: Non-traceable author statement associating SLX4 with DNA replication in a review of SLX4-nuclease complexes. review_file: genes/human/SLX4/SLX4-ai-review.yaml - organism: human gene: SOS1 qualifier: involved_in term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence: IDA reference: PMID:23027131 review_action: MARK_AS_OVER_ANNOTATED review_summary: IDA regulation of transcription by RNA polymerase II from a study of Ras-driven Wnt4 repression and cell motility. review_file: genes/human/SOS1/SOS1-ai-review.yaml - organism: human gene: SOS1 qualifier: involved_in term: id: GO:0042127 label: regulation of cell population proliferation evidence: NAS reference: PMID:38188543 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS regulation of cell population proliferation from a structural/dynamics study of SOS1-KRAS activation. review_file: genes/human/SOS1/SOS1-ai-review.yaml - organism: human gene: SOS1 qualifier: involved_in term: id: GO:0042127 label: regulation of cell population proliferation evidence: IDA reference: PMID:9054499 review_action: MARK_AS_OVER_ANNOTATED review_summary: IDA regulation of cell population proliferation from the study showing oncogenic Ras induces premature senescence. review_file: genes/human/SOS1/SOS1-ai-review.yaml - organism: human gene: SOS1 qualifier: part_of term: id: GO:1905360 label: GTPase complex evidence: IPI reference: PMID:39043660 review_action: MARK_AS_OVER_ANNOTATED review_summary: IPI GTPase complex from a nanobody study of SOS1-RAS complex formation. review_file: genes/human/SOS1/SOS1-ai-review.yaml - organism: human gene: SOS1 qualifier: part_of term: id: GO:1905360 label: GTPase complex evidence: IPI reference: PMID:25695162 review_action: MARK_AS_OVER_ANNOTATED review_summary: IPI GTPase complex from a fragment-screening crystallography study of the Ras:SOS complex. review_file: genes/human/SOS1/SOS1-ai-review.yaml - organism: human gene: STING1 qualifier: involved_in term: id: GO:0045820 label: negative regulation of glycolysis evidence: NAS reference: PMID:40861013 review_action: MARK_AS_OVER_ANNOTATED review_summary: Asserted only as NAS from a 2025 review of non-canonical MITA/STING roles. review_file: genes/human/STING1/STING1-ai-review.yaml - organism: human gene: STING1 qualifier: involved_in term: id: GO:0055088 label: lipid homeostasis evidence: NAS reference: PMID:40861013 review_action: MARK_AS_OVER_ANNOTATED review_summary: Asserted only as NAS from the same 2025 review. review_file: genes/human/STING1/STING1-ai-review.yaml - organism: human gene: SYCE3 qualifier: located_in term: id: GO:0000794 label: condensed nuclear chromosome evidence: NAS reference: PMID:27142324 review_action: MARK_AS_OVER_ANNOTATED review_summary: This annotation from ComplexPortal is based on a review article (Cahoon & Hawley 2016) that discusses SC regulation generally but does not provide SYCE3-specific evidence for localization to condensed chromosomes. The synaptonemal complex assembles during meiotic prophase I when chromosomes are not yet fully condensed, making this term potentially misleading. review_file: genes/human/SYCE3/SYCE3-ai-review.yaml - organism: human gene: TIMM21 qualifier: involved_in term: id: GO:0006886 label: intracellular protein transport evidence: NAS reference: PMID:10339406 review_action: MARK_AS_OVER_ANNOTATED review_summary: Correct pathway family but too broad. TIMM21 is specifically involved in TIM23SORT-mediated mitochondrial inner-membrane protein insertion/sorting. review_file: genes/human/TIMM21/TIMM21-ai-review.yaml - organism: human gene: TIMM23 qualifier: involved_in term: id: GO:0006886 label: intracellular protein transport evidence: NAS reference: PMID:10339406 review_action: MARK_AS_OVER_ANNOTATED review_summary: Correct but broad. TIMM23 is specifically involved in mitochondrial protein import via the TIM23 presequence translocase. review_file: genes/human/TIMM23/TIMM23-ai-review.yaml - organism: human gene: TIMM44 qualifier: involved_in term: id: GO:0006886 label: intracellular protein transport evidence: NAS reference: PMID:10339406 review_action: MARK_AS_OVER_ANNOTATED review_summary: Correct pathway family but too broad. TIMM44 functions in TIM23/PAM-mediated mitochondrial presequence import, not general intracellular protein transport. review_file: genes/human/TIMM44/TIMM44-ai-review.yaml - organism: human gene: TIMM50 qualifier: involved_in term: id: GO:0006886 label: intracellular protein transport evidence: NAS reference: PMID:10339406 review_action: MARK_AS_OVER_ANNOTATED review_summary: Correct pathway family but too broad. TIMM50 specifically mediates TIM23-dependent mitochondrial presequence protein import rather than general intracellular protein transport. review_file: genes/human/TIMM50/TIMM50-ai-review.yaml - organism: human gene: TOMM20 qualifier: involved_in term: id: GO:0045040 label: protein insertion into mitochondrial outer membrane evidence: NAS reference: PMID:18331822 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS annotation to GO:0045040 "protein insertion into mitochondrial outer membrane" from PMID:18331822. This GO term describes the process of inserting proteins from outside the organelle into the mitochondrial outer membrane, mediated by large outer membrane translocase complexes. While the TOM complex does handle some outer membrane proteins, this process is more specifically associated with the SAM complex (GO:0001401) and MIM complex (GO:0140595). TOMM20 primarily recognizes presequence-bearing proteins destined for the matrix and inner membrane, not outer membrane insertion. The TOM complex mediates initial recognition and translocation across the outer membrane, but insertion into the outer membrane is primarily a SAM/MIM function. review_file: genes/human/TOMM20/TOMM20-ai-review.yaml - organism: human gene: TRAF3 qualifier: part_of term: id: GO:1902554 label: serine/threonine protein kinase complex evidence: NAS reference: PMID:24622840 review_action: MARK_AS_OVER_ANNOTATED review_summary: Assignment of TRAF3 to a serine/threonine protein kinase complex, from the STING-TRAF3-TBK1 complex described in a SARS-CoV PLpro study. review_file: genes/human/TRAF3/TRAF3-ai-review.yaml - organism: human gene: UBAP1 qualifier: involved_in term: id: GO:0090148 label: membrane fission evidence: NAS reference: PMID:32424346 review_action: MARK_AS_OVER_ANNOTATED review_summary: Membrane fission is over-transferred for UBAP1 as written. review_file: genes/human/UBAP1/UBAP1-ai-review.yaml - organism: human gene: VPS37C qualifier: involved_in term: id: GO:0090148 label: membrane fission evidence: NAS reference: PMID:32424346 review_action: MARK_AS_OVER_ANNOTATED review_summary: Membrane fission is a broad ESCRT-I mechanism annotation and is over-transferred for VPS37C as written. review_file: genes/human/VPS37C/VPS37C-ai-review.yaml - organism: human gene: VPS37D qualifier: involved_in term: id: GO:0090148 label: membrane fission evidence: NAS reference: PMID:32424346 review_action: MARK_AS_OVER_ANNOTATED review_summary: Membrane fission is a broad ESCRT-I mechanism annotation and is over-transferred for VPS37D as written. review_file: genes/human/VPS37D/VPS37D-ai-review.yaml - organism: human gene: VPS4A qualifier: involved_in term: id: GO:0006914 label: autophagy evidence: NAS reference: PMID:17428789 review_action: MARK_AS_OVER_ANNOTATED review_summary: Autophagy connection is plausible for ESCRT machinery, but the local cached evidence for this specific VPS4A annotation is yeast-only or review-level rather than direct human VPS4A evidence. review_file: genes/human/VPS4A/VPS4A-ai-review.yaml - organism: human gene: VPS4A qualifier: involved_in term: id: GO:0097352 label: autophagosome maturation evidence: NAS reference: PMID:9211789 review_action: MARK_AS_OVER_ANNOTATED review_summary: Autophagy connection is plausible for ESCRT machinery, but the local cached evidence for this specific VPS4A annotation is yeast-only or review-level rather than direct human VPS4A evidence. review_file: genes/human/VPS4A/VPS4A-ai-review.yaml - organism: human gene: VPS4B qualifier: involved_in term: id: GO:0006914 label: autophagy evidence: NAS reference: PMID:17428789 review_action: MARK_AS_OVER_ANNOTATED review_summary: Autophagy connection is plausible for ESCRT machinery, but the local cached evidence for this specific VPS4B annotation is yeast-only or review-level rather than direct human VPS4B evidence. review_file: genes/human/VPS4B/VPS4B-ai-review.yaml - organism: human gene: VPS4B qualifier: involved_in term: id: GO:0097352 label: autophagosome maturation evidence: NAS reference: PMID:9211789 review_action: MARK_AS_OVER_ANNOTATED review_summary: Autophagy connection is plausible for ESCRT machinery, but the local cached evidence for this specific VPS4B annotation is yeast-only or review-level rather than direct human VPS4B evidence. review_file: genes/human/VPS4B/VPS4B-ai-review.yaml - organism: mouse gene: Actb qualifier: located_in term: id: GO:0000776 label: kinetochore evidence: NAS reference: PMID:11078522 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'kinetochore' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0006338 label: chromatin remodeling evidence: NAS reference: PMID:10078207 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'chromatin remodeling' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0006338 label: chromatin remodeling evidence: NAS reference: PMID:29374058 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'chromatin remodeling' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence: NAS reference: PMID:11263494 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'regulation of transcription by RNA polymerase II' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence: NAS reference: PMID:17340523 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'regulation of transcription by RNA polymerase II' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence: NAS reference: PMID:17920018 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'regulation of transcription by RNA polymerase II' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence: NAS reference: PMID:18809673 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'regulation of transcription by RNA polymerase II' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0006357 label: regulation of transcription by RNA polymerase II evidence: NAS reference: PMID:29374058 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'regulation of transcription by RNA polymerase II' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0008284 label: positive regulation of cell population proliferation evidence: NAS reference: PMID:29374058 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'positive regulation of cell population proliferation' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0030071 label: regulation of mitotic metaphase/anaphase transition evidence: NAS reference: PMID:23698369 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'regulation of mitotic metaphase/anaphase transition' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0030071 label: regulation of mitotic metaphase/anaphase transition evidence: NAS reference: PMID:25066234 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'regulation of mitotic metaphase/anaphase transition' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0042981 label: regulation of apoptotic process evidence: NAS reference: PMID:14966270 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'regulation of apoptotic process' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0045582 label: positive regulation of T cell differentiation evidence: NAS reference: PMID:12110891 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'positive regulation of T cell differentiation' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0045596 label: negative regulation of cell differentiation evidence: NAS reference: PMID:30510198 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'negative regulation of cell differentiation' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0045597 label: positive regulation of cell differentiation evidence: NAS reference: PMID:11790558 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'positive regulation of cell differentiation' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0045597 label: positive regulation of cell differentiation evidence: NAS reference: PMID:12368262 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'positive regulation of cell differentiation' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0045663 label: positive regulation of myoblast differentiation evidence: NAS reference: PMID:11175787 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'positive regulation of myoblast differentiation' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0045663 label: positive regulation of myoblast differentiation evidence: NAS reference: PMID:15985610 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'positive regulation of myoblast differentiation' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0045893 label: positive regulation of DNA-templated transcription evidence: NAS reference: PMID:27153538 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'positive regulation of DNA-templated transcription' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:0070316 label: regulation of G0 to G1 transition evidence: NAS reference: PMID:11790558 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'regulation of G0 to G1 transition' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:1902459 label: positive regulation of stem cell population maintenance evidence: NAS reference: PMID:19279220 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'positive regulation of stem cell population maintenance' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:1902459 label: positive regulation of stem cell population maintenance evidence: NAS reference: PMID:30510198 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'positive regulation of stem cell population maintenance' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:2000045 label: regulation of G1/S transition of mitotic cell cycle evidence: NAS reference: PMID:10778858 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'regulation of G1/S transition of mitotic cell cycle' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:2000779 label: regulation of double-strand break repair evidence: NAS reference: PMID:14966270 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'regulation of double-strand break repair' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:2000781 label: positive regulation of double-strand break repair evidence: NAS reference: PMID:16932743 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'positive regulation of double-strand break repair' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:2000781 label: positive regulation of double-strand break repair evidence: NAS reference: PMID:25066234 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'positive regulation of double-strand break repair' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: Actb qualifier: involved_in term: id: GO:2000819 label: regulation of nucleotide-excision repair evidence: NAS reference: PMID:12215535 review_action: MARK_AS_OVER_ANNOTATED review_summary: This 'regulation of nucleotide-excision repair' annotation (NAS) is transferred from studies of chromatin-remodeling complex subunits (SWI/SNF, BAF, PBAF, esBAF, NuA4/TIP60), not from data on cytoplasmic beta-actin itself. While a minor monomeric nuclear actin pool is a shared structural subunit of some of these complexes, attributing these specific differentiation/cell-cycle/DNA-repair/transcription processes to ACTB is an over-annotation arising from complex/paralog confusion. The falcon deep research contains no chromatin-remodeling, SWI/SNF or BAF evidence for beta-actin. review_file: genes/mouse/Actb/Actb-ai-review.yaml - organism: mouse gene: App qualifier: involved_in term: id: GO:1900272 label: negative regulation of long-term synaptic potentiation evidence: IDA reference: PMID:18568035 review_action: MARK_AS_OVER_ANNOTATED review_summary: Abeta oligomers inhibit LTP (PMID:18568035, PMID:19242475). However, this is specifically an Abeta function, not full-length APP. sAPPalpha actually ENHANCES LTP. Annotation conflates opposing functions of different APP products. review_file: genes/mouse/App/App-ai-review.yaml - organism: mouse gene: App qualifier: involved_in term: id: GO:1900272 label: negative regulation of long-term synaptic potentiation evidence: NAS reference: PMID:19242475 review_action: MARK_AS_OVER_ANNOTATED review_summary: Abeta oligomers inhibit LTP (PMID:18568035, PMID:19242475). However, this is specifically an Abeta function, not full-length APP. sAPPalpha actually ENHANCES LTP. Annotation conflates opposing functions of different APP products. review_file: genes/mouse/App/App-ai-review.yaml - organism: mouse gene: App qualifier: involved_in term: id: GO:1900272 label: negative regulation of long-term synaptic potentiation evidence: IDA reference: PMID:18568035 review_action: MARK_AS_OVER_ANNOTATED review_summary: Abeta oligomers inhibit LTP (PMID:18568035, PMID:19242475). However, this is specifically an Abeta function, not full-length APP. sAPPalpha actually ENHANCES LTP. Annotation conflates opposing functions of different APP products. review_file: genes/mouse/App/App-ai-review.yaml - organism: mouse gene: App qualifier: involved_in term: id: GO:1900272 label: negative regulation of long-term synaptic potentiation evidence: NAS reference: PMID:19242475 review_action: MARK_AS_OVER_ANNOTATED review_summary: Abeta oligomers inhibit LTP (PMID:18568035, PMID:19242475). However, this is specifically an Abeta function, not full-length APP. sAPPalpha actually ENHANCES LTP. Annotation conflates opposing functions of different APP products. review_file: genes/mouse/App/App-ai-review.yaml - organism: mouse gene: App qualifier: involved_in term: id: GO:1900454 label: positive regulation of long-term synaptic depression evidence: NAS reference: PMID:19242475 review_action: MARK_AS_OVER_ANNOTATED review_summary: Abeta oligomers enhance LTD via mGluR-dependent mechanism (PMID:18568035, PMID:19242475). This is specifically an Abeta oligomer function, not a property of full-length APP. review_file: genes/mouse/App/App-ai-review.yaml - organism: mouse gene: App qualifier: involved_in term: id: GO:1900454 label: positive regulation of long-term synaptic depression evidence: NAS reference: PMID:19242475 review_action: MARK_AS_OVER_ANNOTATED review_summary: Abeta oligomers enhance LTD via mGluR-dependent mechanism (PMID:18568035, PMID:19242475). This is specifically an Abeta oligomer function, not a property of full-length APP. review_file: genes/mouse/App/App-ai-review.yaml - organism: worm gene: daf-18 qualifier: part_of term: id: GO:0062049 label: protein phosphatase inhibitor complex evidence: NAS reference: PMID:20207731 review_action: MARK_AS_OVER_ANNOTATED review_summary: NAS protein phosphatase inhibitor complex (ARR-1/MPZ-1/DAF-18 complex). review_file: genes/worm/daf-18/daf-18-ai-review.yaml - organism: worm gene: sir-2.1 qualifier: involved_in term: id: GO:0010468 label: regulation of gene expression evidence: NAS reference: PMID:16777605 review_action: MARK_AS_OVER_ANNOTATED review_summary: General regulation of gene expression through chromatin modification and transcription factor interactions. review_file: genes/worm/sir-2.1/sir-2.1-ai-review.yaml - organism: yeast gene: CAC2 qualifier: involved_in term: id: GO:0006260 label: DNA replication evidence: NAS reference: PMID:30239791 review_action: MARK_AS_OVER_ANNOTATED review_summary: Complex Portal NAS annotation of CAC2/CAF-1 to the broad process DNA replication. review_file: genes/yeast/CAC2/CAC2-ai-review.yaml - organism: yeast gene: CDC14 qualifier: involved_in term: id: GO:0000183 label: rDNA heterochromatin formation evidence: NAS reference: PMID:12923057 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'NAS annotation derived from the RENT-complex literature: RENT (Net1-Sir2-Cdc14) mediates rDNA silencing, but the silencing work is done by the Sir2 deacetylase recruited through Net1/Fob1; no experiment shows that Cdc14 phosphatase activity contributes to rDNA heterochromatin formation, and the cited paper does not examine Cdc14.' review_file: genes/yeast/CDC14/CDC14-ai-review.yaml - organism: yeast gene: CDC53 qualifier: involved_in term: id: GO:0010828 label: positive regulation of D-glucose transmembrane transport evidence: IDA reference: PMID:10213692 review_action: MARK_AS_OVER_ANNOTATED review_summary: SCF(Grr1), built on Cdc53 and Skp1, is required for glucose induction of the HXT glucose-transporter genes; the cited paper reconstitutes Cln1 ubiquitination by SCF(Grr1)-Rbx1 and does not itself address glucose transport. review_file: genes/yeast/CDC53/CDC53-ai-review.yaml - organism: yeast gene: CDC53 qualifier: involved_in term: id: GO:0071406 label: cellular response to methylmercury evidence: NAS reference: PMID:17141224 review_action: MARK_AS_OVER_ANNOTATED review_summary: Overexpression of the F-box proteins Hrt3 or Ylr224w confers methylmercury resistance, apparently by enhancing proteasomal degradation of a toxicity-enhancing protein; Cdc53 is inferred to be the cullin of those SCFs. review_file: genes/yeast/CDC53/CDC53-ai-review.yaml - organism: yeast gene: HAP4 qualifier: involved_in term: id: GO:0006109 label: regulation of carbohydrate metabolic process evidence: NAS reference: PMID:16278450 review_action: MARK_AS_OVER_ANNOTATED review_summary: HAP4 is annotated with regulation of carbohydrate metabolism. While HAP4 responds to glucose/carbohydrate availability through glucose-repressible expression, it does not directly regulate carbohydrate metabolic enzymes. Instead, it activates respiratory/mitochondrial genes that oxidize carbohydrates. The annotation conflates metabolic context with direct molecular targets. review_file: genes/yeast/HAP4/HAP4-ai-review.yaml - organism: yeast gene: HRT1 qualifier: involved_in term: id: GO:0006334 label: nucleosome assembly evidence: NAS reference: PMID:20139071 review_action: MARK_AS_OVER_ANNOTATED review_summary: Author statement from the Cul8/Rtt101 complex paper, which shows Cul8 interacting with replication and silencing factors (Esc4, Ctf4, Esc2, Orc5) but contains no nucleosome-assembly assay; later work on Rtt101(Mms1-Mms22) ubiquitylation of new histone H3 is not in the cache. review_file: genes/yeast/HRT1/HRT1-ai-review.yaml - organism: yeast gene: HRT1 qualifier: involved_in term: id: GO:0010828 label: positive regulation of D-glucose transmembrane transport evidence: IDA reference: PMID:10213692 review_action: MARK_AS_OVER_ANNOTATED review_summary: SCF(Grr1) is required for glucose induction of the HXT glucose-transporter genes; the cited paper reconstitutes Cln1 ubiquitination by SCF(Grr1)-Rbx1 and does not address glucose transport. review_file: genes/yeast/HRT1/HRT1-ai-review.yaml - organism: yeast gene: HRT1 qualifier: involved_in term: id: GO:0031507 label: heterochromatin formation evidence: NAS reference: PMID:20139071 review_action: MARK_AS_OVER_ANNOTATED review_summary: cul8-delta, mms1-delta, mms22-delta and ctf4-delta cells lose telomeric URA3 silencing; the authors speculate that Cul8 is loaded onto telomeric chromatin through Ctf4. The heterochromatin term was transferred to Hrt1 as the RING of the Cul8 complex. review_file: genes/yeast/HRT1/HRT1-ai-review.yaml - organism: yeast gene: HRT1 qualifier: involved_in term: id: GO:0071406 label: cellular response to methylmercury evidence: NAS reference: PMID:17141224 review_action: MARK_AS_OVER_ANNOTATED review_summary: Overexpression of the F-box proteins Hrt3 or Ylr224w confers methylmercury resistance, apparently by enhancing proteasomal degradation of an unidentified toxicity-enhancing protein; Hrt1 is inferred to be the RING of those SCFs. review_file: genes/yeast/HRT1/HRT1-ai-review.yaml - organism: yeast gene: MSI1 qualifier: involved_in term: id: GO:0006260 label: DNA replication evidence: NAS reference: PMID:30239791 review_action: MARK_AS_OVER_ANNOTATED review_summary: Complex Portal NAS annotation of MSI1/CAF-1 to the broad process DNA replication. review_file: genes/yeast/MSI1/MSI1-ai-review.yaml - organism: yeast gene: RCO1 qualifier: involved_in term: id: GO:0006334 label: nucleosome assembly evidence: NAS reference: PMID:22177115 review_action: MARK_AS_OVER_ANNOTATED review_summary: The Rpd3 core complex is described as a "chromatin stabilization module" that maintains nucleosome integrity and prevents nucleosome eviction. This could be interpreted as related to nucleosome assembly, though it is more accurately described as nucleosome maintenance and stabilization. review_file: genes/yeast/RCO1/RCO1-ai-review.yaml - organism: yeast gene: RLF2 qualifier: involved_in term: id: GO:0006260 label: DNA replication evidence: NAS reference: PMID:30239791 review_action: MARK_AS_OVER_ANNOTATED review_summary: Complex Portal NAS annotation of RLF2/CAF-1 to the broad process DNA replication. review_file: genes/yeast/RLF2/RLF2-ai-review.yaml - organism: yeast gene: SAS3 qualifier: involved_in term: id: GO:0006351 label: DNA-templated transcription evidence: NAS reference: PMID:17157260 review_action: MARK_AS_OVER_ANNOTATED review_summary: This process term is broader than the specific mechanistic role supported for SAS3. review_file: genes/yeast/SAS3/SAS3-ai-review.yaml - organism: yeast gene: SER3 qualifier: involved_in term: id: GO:0006979 label: response to oxidative stress evidence: NAS reference: PMID:26527276 review_action: MARK_AS_OVER_ANNOTATED review_summary: A complex-level annotation propagated to a subunit. This row is assigned by ComplexPortal (SER3-goa.tsv:14), which curates the SESAME metabolic enzyme complex CPX-9181; UniProt records Ser3p's membership of that complex at SER3-uniprot.txt:99. The property being annotated belongs to SESAME as a whole, and reaches Ser3p only by virtue of subunit membership, not because Ser3p's own 3-phosphoglycerate dehydrogenase activity was shown to participate in an oxidative-stress response. review_file: genes/yeast/SER3/SER3-ai-review.yaml - organism: yeast gene: SER3 qualifier: involved_in term: id: GO:0040029 label: epigenetic regulation of gene expression evidence: NAS reference: PMID:26527276 review_action: MARK_AS_OVER_ANNOTATED review_summary: This appears to be based on the SESAME complex study linking serine metabolism to histone modifications. However, this is an indirect connection through metabolite availability rather than a direct function of SER3. The primary function of SER3 is serine biosynthesis. review_file: genes/yeast/SER3/SER3-ai-review.yaml - organism: yeast gene: SER3 qualifier: part_of term: id: GO:1902494 label: catalytic complex evidence: NAS reference: PMID:26527276 review_action: MARK_AS_OVER_ANNOTATED review_summary: This cellular component term is too generic. Ser3p is reported as part of the SESAME catalytic complex, but the annotation does not provide a specific, informative localization or complex name. review_file: genes/yeast/SER3/SER3-ai-review.yaml - organism: yeast gene: SKP1 qualifier: involved_in term: id: GO:0010828 label: positive regulation of D-glucose transmembrane transport evidence: IDA reference: PMID:10213692 review_action: MARK_AS_OVER_ANNOTATED review_summary: ComplexPortal row for SCF(Grr1) recording the Grr1-dependent induction of HXT glucose-transporter genes; the cited paper reconstitutes Cln1 ubiquitination and does not address glucose transport. review_file: genes/yeast/SKP1/SKP1-ai-review.yaml - organism: yeast gene: SKP1 qualifier: involved_in term: id: GO:0071406 label: cellular response to methylmercury evidence: NAS reference: PMID:17141224 review_action: MARK_AS_OVER_ANNOTATED review_summary: 'ComplexPortal row for SCF(Hrt3)/SCF(Ucc1): overexpression of the F-box proteins Hrt3 or Ylr224w (Ucc1) confers proteasome-dependent methylmercury resistance.' review_file: genes/yeast/SKP1/SKP1-ai-review.yaml