IRD evidence: results
Generated by analyze_ird.py; do not edit by hand.
1. IRD node annotations in PAINT
2538 IRD rows on 1539 nodes in 894 PANTHER families. All are negated: 2538 ({'NOT': 2524, 'NOT|contributes_to': 14}).
| Aspect | IRD rows |
|---|---|
| BP | 968 |
| MF | 850 |
| CC | 720 |
- 150 IRD rows share their ancestor and term with an IKR loss elsewhere in the tree.
- 14 IRD rows point at an ancestral node that no longer has an IBD for the term (stale overrides):
| Family | IRD node | Term | Ancestral node |
|---|---|---|---|
| PTHR11802 | PTN001720128 | GO:0005773 vacuole | PTN001720040 |
| PTHR12260 | PTN000262554 | GO:0005634 nucleus | PTN000262496 |
| PTHR12897 | PTN000984912 | GO:0005765 lysosomal membrane | PTN000307264 |
| PTHR12919 | PTN002293408 | GO:0032543 mitochondrial translation | PTN000308745 |
| PTHR13681 | PTN002299200 | GO:0000381 regulation of alternative mRNA splicing, via spliceosome | PTN001784834 |
| PTHR24261 | PTN001546628 | GO:0031012 extracellular matrix | PTN002799862 |
| PTHR33269 | PTN002115829 | GO:0045271 respiratory chain complex I | PTN004990314 |
| PTHR43048 | PTN000482983 | GO:0005739 mitochondrion | PTN001468099 |
| PTHR43782 | PTN002886720 | GO:0005634 nucleus | PTN000144387 |
| PTHR43795 | PTN008453022 | GO:0009507 chloroplast | PTN008453015 |
| PTHR45639 | PTN009180209 | GO:0030968 endoplasmic reticulum unfolded protein response | PTN000452651 |
| PTHR45688 | PTN000241152 | GO:0005739 mitochondrion | PTN000241036 |
| PTHR45688 | PTN000241488 | GO:0005739 mitochondrion | PTN000241036 |
| PTHR46590 | PTN008709838 | GO:0005739 mitochondrion | PTN008709837 |
Top MF terms blocked by IRD:
| Term | IRD rows |
|---|---|
| GO:0003924 GTPase activity | 74 |
| GO:0004222 metalloendopeptidase activity | 43 |
| GO:0004674 protein serine/threonine kinase activity | 19 |
| GO:0005200 structural constituent of cytoskeleton | 11 |
| GO:0003904 deoxyribodipyrimidine photo-lyase activity | 10 |
| GO:0003735 structural constituent of ribosome | 10 |
| GO:0004792 thiosulfate-cyanide sulfurtransferase activity | 9 |
| GO:0004197 cysteine-type endopeptidase activity | 8 |
| GO:0016779 nucleotidyltransferase activity | 8 |
| GO:0038023 signaling receptor activity | 8 |
| GO:0008745 N-acetylmuramoyl-L-alanine amidase activity | 7 |
| GO:0004568 chitinase activity | 6 |
Top BP terms blocked by IRD:
| Term | IRD rows |
|---|---|
| GO:0006508 proteolysis | 21 |
| GO:0030198 extracellular matrix organization | 16 |
| GO:0045036 protein targeting to chloroplast | 9 |
| GO:0045037 protein import into chloroplast stroma | 9 |
| GO:0006414 translational elongation | 9 |
| GO:0006915 apoptotic process | 8 |
| GO:0000398 mRNA splicing, via spliceosome | 8 |
| GO:0006368 transcription elongation by RNA polymerase II | 8 |
| GO:0007165 signal transduction | 8 |
| GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process | 7 |
| GO:0006355 regulation of DNA-templated transcription | 7 |
| GO:0007346 regulation of mitotic cell cycle | 7 |
Top CC terms blocked by IRD:
| Term | IRD rows |
|---|---|
| GO:0005739 mitochondrion | 72 |
| GO:0005886 plasma membrane | 71 |
| GO:0005634 nucleus | 57 |
| GO:0005829 cytosol | 52 |
| GO:0005783 endoplasmic reticulum | 17 |
| GO:0031012 extracellular matrix | 16 |
| GO:0005737 cytoplasm | 15 |
| GO:0005576 extracellular region | 12 |
| GO:0022625 cytosolic large ribosomal subunit | 12 |
| GO:0005813 centrosome | 11 |
| GO:0005689 U12-type spliceosomal complex | 10 |
| GO:0005789 endoplasmic reticulum membrane | 9 |
IRD rows by annotation year:
| Year | Rows |
|---|---|
| 2017 | 46 |
| 2018 | 53 |
| 2019 | 32 |
| 2020 | 61 |
| 2021 | 89 |
| 2022 | 92 |
| 2023 | 114 |
| 2024 | 438 |
| 2025 | 577 |
| 2026 | 1036 |
Families with the most IRD rows:
| Family | IRD rows |
|---|---|
| PTHR10903 | 100 |
| PTHR13723 | 57 |
| PTHR11733 | 24 |
| PTHR10131 | 20 |
| PTHR10953 | 19 |
| PTHR24057 | 19 |
| PTHR10454 | 18 |
| PTHR19443 | 17 |
| PTHR12732 | 16 |
| PTHR18966 | 15 |
2. Do IRD calls reach leaf genes?
Leaf IBA rows in gene_association.paint_uniprot.gaf.gz, tallied by which losses sit on the ancestor+term the row was projected from:
| Leaf polarity | Losses on source ancestor+term | Leaf rows |
|---|---|---|
| NOT | IKR | 2170 |
| NOT | IKR+IRD | 459 |
| NOT | none | 252 |
| positive | IKR | 38145 |
| positive | IKR+IRD | 26336 |
| positive | IRD | 333738 |
| positive | none | 4237445 |
NOT leaf rows whose only source loss is an IRD: 0. IRD therefore never produces a NOT|IBA; it only stops the ancestral IBD descending.
3. IRD clades
52660 (IRD row, leaf) pairs; 33633 distinct UniProt accessions (678 human). 0 IRD rows could not be resolved to leaves.
| Leaves under the IRD node | IRD rows |
|---|---|
| 1 (leaf) | 789 |
| 2-10 | 599 |
| 11-100 | 1048 |
| >100 | 102 |
PAINT re-annotates part of the clade below the IRD node: 847 (IRD row, protein) pairs still receive a positive IBA for the blocked term or a descendant. 31 IRD rows are partly re-annotated, 20 fully (the IRD then blocks nothing on these leaves).
4. Experimental annotations inside IRD clades
Experimental GOA annotations downloaded for clade members: 34438 rows on 2909 proteins.
- Positive experimental annotations to the blocked term or a GO descendant: 463 rows; 118 of them are on proteins PAINT re-annotates below the IRD node, and are not conflicts.
- Inside the effective block: 345 rows, 237 (IRD, protein) pairs, touching 170 of 2538 IRD rows (6.7%); 157 IRD rows have at least one low-throughput conflict.
- NOT experimental annotations agreeing with the block: 205 rows on 165 IRD rows.
| Aspect | Conflicting rows | IRD rows conflicted | IRD rows in aspect | Share |
|---|---|---|---|---|
| MF | 138 | 63 | 850 | 7.4% |
| BP | 80 | 45 | 968 | 4.6% |
| CC | 127 | 62 | 720 | 8.6% |
Conflicting rows by evidence code:
| Evidence | Rows |
|---|---|
| IDA | 209 |
| IMP | 55 |
| HDA | 34 |
| EXP | 29 |
| IGI | 11 |
| IPI | 7 |
Conflicting rows by relation:
| Relation | Rows |
|---|---|
| enables | 148 |
| located_in | 90 |
| involved_in | 56 |
| part_of | 31 |
| acts_upstream_of_or_within | 10 |
| is_active_in | 5 |
| contributes_to | 4 |
| colocalizes_with | 1 |
IRD rows with the most proteins carrying a low-throughput experimental positive (worklist):
| Family | IRD node | Aspect | Blocked term | Clade size | Proteins with experimental positive |
|---|---|---|---|---|---|
| PTHR10210 | PTN000025038 | CC | GO:0002189 ribose phosphate diphosphokinase complex | 133 | 7: PRS2 (Saccharomyces cerevisiae), PRS3 (Saccharomyces cerevisiae), PRS4 (Saccharomyces cerevisiae), PRS5 (Saccharomyces cerevisiae), Prps2 (Rattus norvegicus), Prpsap1 (Rattus norvegicus) ... |
| PTHR11588 | PTN000172659 | CC | GO:0005874 microtubule | 134 | 7: TUBG1 (Arabidopsis thaliana), TUBG1 (Homo sapiens), TUBG2 (Arabidopsis thaliana), TUBG2 (Homo sapiens), Tubg1 (Mus musculus), Tubg2 (Mus musculus) ... |
| PTHR11309 | PTN002259328 | CC | GO:0005886 plasma membrane | 156 | 6: FZD9 (Homo sapiens), Fzd10 (Mus musculus), Fzd9 (Mus musculus), Fzd9 (Rattus norvegicus), SFRP1 (Bos taurus), lin-17 (Caenorhabditis elegans) |
| PTHR23086 | PTN001132453 | MF | GO:0016308 1-phosphatidylinositol-4-phosphate 5-kinase activity | 77 | 5: LOC560360 (Danio rerio), PIP4K2A (Homo sapiens), PIP4K2B (Homo sapiens), PIP4K2C (Homo sapiens), Pip4k2c (Rattus norvegicus) |
| PTHR23359 | PTN000599579 | MF | GO:0004017 AMP kinase activity | 262 | 4: AK9 (Homo sapiens), Cmpk (Drosophila melanogaster), Tb09.211.0350 (Trypanosoma brucei), URA6 (Saccharomyces cerevisiae) |
| PTHR24056 | PTN000756102 | MF | GO:0004674 protein serine/threonine kinase activity | 40 | 4: CDKL5 (Homo sapiens), Cdkl5 (Danio rerio), Cdkl5 (Mus musculus), YGK3 (Saccharomyces cerevisiae) |
| PTHR11309 | PTN002259328 | MF | GO:0042813 Wnt receptor activity | 156 | 4: FZD10 (Homo sapiens), Fzd9 (Mus musculus), Fzd9 (Rattus norvegicus), fk48e04 (Danio rerio) |
| PTHR10625 | PTN008492157 | MF | GO:0004407 histone deacetylase activity | 42 | 4: HDAC10 (Homo sapiens), HDAC6 (Drosophila melanogaster), HDAC6 (Homo sapiens), Hdac6 (Mus musculus) |
| PTHR10638 | PTN000067358 | MF | GO:0008131 primary methylamine oxidase activity | 21 | 3: AOC3 (Homo sapiens), Aoc3 (Mus musculus), Aoc3 (Rattus norvegicus) |
| PTHR24056 | PTN000623095 | CC | GO:0016592 mediator complex | 60 | 3: CDK8 (Homo sapiens), Cdk8 (Drosophila melanogaster), Cdk8 (Mus musculus) |
| PTHR10694 | PTN000075209 | MF | GO:0051864 histone H3K36 demethylase activity | 45 | 2: KDM4B (Homo sapiens), Kdm4b (Mus musculus) |
| PTHR11207 | PTN000129456 | BP | GO:0010468 regulation of gene expression | 96 | 2: DCR1 (Candida albicans), pac1 (Schizosaccharomyces pombe) |
| PTHR11588 | PTN000172659 | MF | GO:0005200 structural constituent of cytoskeleton | 134 | 2: TUB4 (Saccharomyces cerevisiae), mipA (Emericella nidulans) |
| PTHR24068 | PTN000629507 | MF | GO:0061631 ubiquitin conjugating enzyme activity | 219 | 2: Ube2v1 (Mus musculus), mms2 (Schizosaccharomyces pombe) |
| PTHR45618 | PTN000642212 | MF | GO:0017077 oxidative phosphorylation uncoupler activity | 15 | 2: UCP3 (Homo sapiens), Ucp3 (Mus musculus) |
| PTHR24103 | PTN000715044 | CC | GO:0005737 cytoplasm | 12 | 2: TRIM41 (Homo sapiens), Trim41 (Mus musculus) |
| PTHR11405 | PTN000892150 | MF | GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity | 13 | 2: CPA2 (Saccharomyces cerevisiae), arg-3 (Neurospora crassa) |
| PTHR11671 | PTN000912638 | CC | GO:0005774 vacuolar membrane | 45 | 2: ATP6V1D (Bos taurus), ATP6V1D (Homo sapiens) |
| PTHR12369 | PTN000961885 | MF | GO:0008376 acetylgalactosaminyltransferase activity | 54 | 2: CHPF (Homo sapiens), Chpf (Mus musculus) |
| PTHR19139 | PTN001452348 | BP | GO:0006833 water transport | 10 | 2: AQP6 (Homo sapiens), Aqp6 (Rattus norvegicus) |
| PTHR19139 | PTN001452348 | MF | GO:0015250 water channel activity | 10 | 2: AQP6 (Homo sapiens), Aqp6 (Rattus norvegicus) |
| PTHR10057 | PTN001600146 | CC | GO:0005741 mitochondrial outer membrane | 16 | 2: Tspo (Mus musculus), Tspo (Rattus norvegicus) |
| PTHR45619 | PTN001705193 | CC | GO:0005829 cytosol | 49 | 2: PP2A1 (Arabidopsis thaliana), PP2A2 (Arabidopsis thaliana) |
| PTHR18966 | PTN001826347 | BP | GO:0035249 synaptic transmission, glutamatergic | 7 | 2: DmelCG11155 (Drosophila melanogaster), Ekar (Drosophila melanogaster) |
| PTHR12247 | PTN002640813 | CC | GO:0035102 PRC1 complex | 33 | 2: Samd11 (Mus musculus), Samd7 (Mus musculus) |
| PTHR19878 | PTN002716574 | CC | GO:0034274 Atg12-Atg5-Atg16 complex | 16 | 2: ATG16L2 (Homo sapiens), Atg16l2 (Mus musculus) |
| PTHR47958 | PTN002773962 | MF | GO:0003724 RNA helicase activity | 208 | 2: DBP2 (Saccharomyces cerevisiae), DDX5 (Homo sapiens) |
| PTHR24229 | PTN002796263 | BP | GO:0007218 neuropeptide signaling pathway | 56 | 2: AstC-R1 (Drosophila melanogaster), AstC-R2 (Drosophila melanogaster) |
| PTHR24361 | PTN007798220 | MF | GO:0004674 protein serine/threonine kinase activity | 10 | 2: Nek6 (Mus musculus), Nek6 (Rattus norvegicus) |
| PTHR10625 | PTN008492157 | CC | GO:0000118 histone deacetylase complex | 42 | 2: HDAC10 (Homo sapiens), HDAC6 (Homo sapiens) |
| PTHR24115 | PTN008606205 | BP | GO:0007019 microtubule depolymerization | 3 | 2: klp5 (Schizosaccharomyces pombe), klp6 (Schizosaccharomyces pombe) |
| PTHR10030 | PTN000003216 | MF | GO:0004560 alpha-L-fucosidase activity | 1 | 1: Fuca (Drosophila melanogaster) |
| PTHR10126 | PTN000013141 | MF | GO:0016251 RNA polymerase II general transcription initiation factor activity | 39 | 1: TBPL1 (Homo sapiens) |
| PTHR10134 | PTN000015359 | CC | GO:0005886 plasma membrane | 170 | 1: RIP1 (Candida albicans) |
| PTHR10196 | PTN000023394 | CC | GO:0005829 cytosol | 189 | 1: Gk (Mus musculus) |
| PTHR10454 | PTN000047958 | CC | GO:0031265 CD95 death-inducing signaling complex | 6 | 1: Cflar (Rattus norvegicus) |
| PTHR10648 | PTN000068762 | CC | GO:0005829 cytosol | 1 | 1: PP2AA3 (Arabidopsis thaliana) |
| PTHR14167 | PTN000070286 | MF | GO:0030674 protein-macromolecule adaptor activity | 66 | 1: Sh3rf1 (Mus musculus) |
| PTHR10696 | PTN000075565 | BP | GO:0045329 carnitine biosynthetic process | 10 | 1: gbh-1 (Caenorhabditis elegans) |
| PTHR45625 | PTN000116766 | MF | GO:0003755 peptidyl-prolyl cis-trans isomerase activity | 105 | 1: cyn-16 (Caenorhabditis elegans) |
5. Our gene reviews inside IRD clades
- 191 reviews cover a protein inside an IRD clade (314 (review, blocked term) pairs).
- 81 pairs: the review annotates the blocked term or a descendant (24 as a core function); 79 of these are inside the effective block (not re-annotated below the IRD by PAINT).
| Review | Blocked term | Aspect | Clade | Review use | Exp. positive in GOA | PAINT re-annotates below |
|---|---|---|---|---|---|---|
| MAM3 (ARATH) | GO:0009098 L-leucine biosynthetic process | BP | 1 | GO:0009098/TAS:MARK_AS_OVER_ANNOTATED | false | false |
| smad3a (DANRE) | GO:0030509 BMP signaling pathway | BP | 58 | GO:0030509/IEA:MARK_AS_OVER_ANNOTATED | false | false |
| smad3b (DANRE) | GO:0030509 BMP signaling pathway | BP | 58 | GO:0030509/IEA:MARK_AS_OVER_ANNOTATED | false | false |
| Buffy (DROME) | GO:0043066 negative regulation of apoptotic process | BP | 7 | GO:0043066/IMP:ACCEPT; GO:0043066/IGI:ACCEPT; GO:0043066:CORE_FUNCTION | false | false |
| cia30 (NEUCR) | GO:0010257 NADH dehydrogenase complex assembly | BP | 11 | GO:0010257/IBA:ACCEPT; GO:0032981/NAS:ACCEPT; GO:0032981:CORE_FUNCTION | false | false |
| cia30 (NEUCR) | GO:0032981 mitochondrial respiratory chain complex I assembly | BP | 11 | GO:0032981/NAS:ACCEPT; GO:0032981:CORE_FUNCTION | false | false |
| mad3 (SCHPO) | GO:0000776 kinetochore | CC | 1 | GO:0000776/NAS:ACCEPT; GO:0000776/NAS:ACCEPT; GO:0000776:CORE_FUNCTION | false | false |
| pmp20 (SCHPO) | GO:0005739 mitochondrion | CC | 13 | GO:0005739/IBA:UNDECIDED | false | false |
| pmp20 (SCHPO) | GO:0005777 peroxisome | CC | 13 | GO:0005777/IBA:UNDECIDED | false | false |
| pmp20 (SCHPO) | GO:0008379 thioredoxin peroxidase activity | MF | 13 | GO:0008379/IBA:REMOVE | false | false |
| pmp20 (SCHPO) | GO:0034599 cellular response to oxidative stress | BP | 13 | GO:0034599/IBA:KEEP_AS_NON_CORE; GO:0034599/IEA:KEEP_AS_NON_CORE | false | false |
| pmp20 (SCHPO) | GO:0042744 hydrogen peroxide catabolic process | BP | 13 | GO:0042744/IBA:REMOVE; NOT GO:0042744/EXP:ACCEPT | false | false |
| pmp20 (SCHPO) | GO:0045454 cell redox homeostasis | BP | 13 | GO:0045454/IBA:UNDECIDED | false | false |
| ste9 (SCHPO) | GO:0005680 anaphase-promoting complex | CC | 1 | GO:0005680/IDA:NEW | false | false |
| ste9 (SCHPO) | GO:0010997 anaphase-promoting complex binding | MF | 1 | GO:0010997/IEA:ACCEPT; GO:0010997:CORE_FUNCTION | false | false |
| A0A3B6NKR6 (WHEAT) | GO:0019287 isopentenyl diphosphate biosynthetic process, mevalonate pathway | BP | 44 | GO:0019287/IEA:MARK_AS_OVER_ANNOTATED | false | false |
| ABCB4 (human) | GO:0055085 transmembrane transport | BP | 10 | GO:0042626/IBA:ACCEPT; GO:0042626/IDA:ACCEPT; GO:0042626/IMP:ACCEPT; GO:0042626/TAS:ACCEPT; GO:0055085/IEA:ACCEPT; GO:0055085/TAS:ACCEPT; GO:0140359/IEA:ACCEPT | false | true |
| ACTL7A (human) | GO:0005200 structural constituent of cytoskeleton | MF | 37 | GO:0005200/TAS:REMOVE | false | false |
| ACTL7B (human) | GO:0005200 structural constituent of cytoskeleton | MF | 37 | GO:0005200/TAS:REMOVE | false | false |
| ACTR1A (human) | GO:0005200 structural constituent of cytoskeleton | MF | 96 | GO:0005200/IDA:NEW; GO:0005200:CORE_FUNCTION | false | false |
| ACTR1B (human) | GO:0005200 structural constituent of cytoskeleton | MF | 96 | GO:0005200:CORE_FUNCTION | false | false |
| ADAMTSL1 (human) | GO:0030198 extracellular matrix organization | BP | 43 | GO:0030198/IEA:KEEP_AS_NON_CORE | false | false |
| ADAMTSL1 (human) | GO:0031012 extracellular matrix | CC | 1 | GO:0031012/IDA:NEW; GO:0031012:CORE_FUNCTION | false | false |
| ADAMTSL3 (human) | GO:0030198 extracellular matrix organization | BP | 43 | GO:0030198/IEA:ACCEPT; GO:0030198:CORE_FUNCTION | false | false |
| ADAMTSL5 (human) | GO:0030198 extracellular matrix organization | BP | 25 | GO:0030198/IEA:MARK_AS_OVER_ANNOTATED | false | false |
| AGO1 (human) | GO:0004521 RNA endonuclease activity | MF | 21 | NOT GO:0004521/IDA:ACCEPT | false | false |
| AK4P3 (human) | GO:0004017 AMP kinase activity | MF | 27 | GO:0004017/IEA:ACCEPT; GO:0004017:CORE_FUNCTION | false | false |
| AK4P3 (human) | GO:0046899 nucleoside triphosphate adenylate kinase activity | MF | 27 | GO:0046899/IEA:ACCEPT | false | false |
| ANO10 (human) | GO:0017128 phospholipid scramblase activity | MF | 66 | GO:0017128/IDA:NEW; GO:0017128:CORE_FUNCTION | false | false |
| ANO10 (human) | GO:0045332 phospholipid translocation | BP | 66 | GO:0017128/IDA:NEW; GO:0017128:CORE_FUNCTION | false | false |
| ANO5 (human) | GO:0017128 phospholipid scramblase activity | MF | 23 | GO:0017128/IDA:NEW; GO:0017128:CORE_FUNCTION | false | false |
| ATG16L2 (human) | GO:0000045 autophagosome assembly | BP | 16 | NOT GO:0000045/ISS:ACCEPT | false | false |
| ATG16L2 (human) | GO:0034274 Atg12-Atg5-Atg16 complex | CC | 16 | GO:0034274/IEA:ACCEPT; GO:0034274/IPI:ACCEPT | true | false |
| ATP1B4 (human) | GO:0005890 sodium:potassium-exchanging ATPase complex | CC | 21 | GO:0005890/IEA:REMOVE | false | false |
| ATP6V1D (human) | GO:0005774 vacuolar membrane | CC | 45 | GO:0005765/IEA:ACCEPT; GO:0005765/IDA:ACCEPT; GO:0046611/IDA:ACCEPT; GO:0005765/NAS:ACCEPT; GO:0000221/ISS:ACCEPT; GO:0005765/HDA:ACCEPT; GO:0005765:CORE_FUNCTION; GO:0005765:CORE_FUNCTION | true | false |
| BPGM (human) | GO:0004619 phosphoglycerate mutase activity | MF | 24 | GO:0004619/IEA:KEEP_AS_NON_CORE | false | false |
| BTF3L4 (human) | GO:0005854 nascent polypeptide-associated complex | CC | 34 | GO:0005854/IPI:NEW | false | false |
| C1GALT1C1 (human) | GO:0016263 N-acetylgalactosaminide beta-1,3-galactosyltransferase activity | MF | 26 | NOT GO:0016263/IMP:ACCEPT | false | false |
| CACNA1G (human) | GO:0008331 high voltage-gated calcium channel activity | MF | 23 | GO:0008331/IBA:MODIFY | false | false |
| CALR3 (human) | GO:0005509 calcium ion binding | MF | 13 | NOT GO:0005509/IDA:ACCEPT | false | false |
| CASP14 (human) | GO:0043525 positive regulation of neuron apoptotic process | BP | 24 | GO:0043525/IBA:REMOVE | false | false |
| CFLAR (human) | GO:0004197 cysteine-type endopeptidase activity | MF | 6 | GO:0004197/IBA:REMOVE; GO:0004197/IEA:REMOVE | false | false |
| CFLAR (human) | GO:0030225 macrophage differentiation | BP | 6 | GO:0030225/IBA:MARK_AS_OVER_ANNOTATED | false | false |
| CFLAR (human) | GO:0031265 CD95 death-inducing signaling complex | CC | 6 | GO:0031265/IBA:ACCEPT; GO:0031265/IEA:ACCEPT | false | false |
| CFLAR (human) | GO:0043525 positive regulation of neuron apoptotic process | BP | 6 | GO:0043525/IBA:REMOVE | false | false |
| CPT1C (human) | GO:0004095 carnitine O-palmitoyltransferase activity | MF | 17 | NOT GO:0004095/ISS:ACCEPT | false | false |
| CPT1C (human) | GO:0005739 mitochondrion | CC | 17 | NOT GO:0005739/ISS:ACCEPT | false | false |
| CRY1 (human) | GO:0003904 deoxyribodipyrimidine photo-lyase activity | MF | 73 | NOT GO:0003904/IDA:ACCEPT | false | false |
| CRY2 (human) | GO:0003904 deoxyribodipyrimidine photo-lyase activity | MF | 73 | NOT GO:0003904/IDA:ACCEPT | false | false |
| CWC27 (human) | GO:0003755 peptidyl-prolyl cis-trans isomerase activity | MF | 105 | NOT GO:0003755/IDA:ACCEPT | false | false |
| GTPBP2 (human) | GO:0003746 translation elongation factor activity | MF | 36 | NOT GO:0003746/IDA:ACCEPT | false | false |
| HDAC6 (human) | GO:0000118 histone deacetylase complex | CC | 42 | GO:0000118/IEA:MARK_AS_OVER_ANNOTATED; GO:0000118/IDA:KEEP_AS_NON_CORE | true | false |
| HDAC6 (human) | GO:0004407 histone deacetylase activity | MF | 42 | GO:0004407/IEA:MARK_AS_OVER_ANNOTATED; GO:0004407/IMP:MODIFY; GO:0004407/IDA:MODIFY | true | false |
| HDAC6 (human) | GO:0040029 epigenetic regulation of gene expression | BP | 42 | GO:0045814/IMP:KEEP_AS_NON_CORE | true | false |
| IDH3B (human) | GO:0004449 isocitrate dehydrogenase (NAD+) activity | MF | 80 | GO:0004449/TAS:REMOVE | false | false |
| IL36RN (human) | GO:0005125 cytokine activity | MF | 12 | GO:0005125/IEA:ACCEPT | false | false |
| ILK (human) | GO:0004674 protein serine/threonine kinase activity | MF | 25 | NOT GO:0004674/IDA:ACCEPT; NOT GO:0004674/IDA:ACCEPT | false | false |
| KL (human) | GO:0008422 beta-glucosidase activity | MF | 126 | GO:0008422/TAS:REMOVE | false | false |
| MOCS3 (human) | GO:0032446 protein modification by small protein conjugation | BP | 126 | GO:0032447/IBA:KEEP_AS_NON_CORE | false | true |
| MTHFD1L (human) | GO:0035999 tetrahydrofolate interconversion | BP | 20 | GO:0035999/IEA:ACCEPT | false | false |
| RPIA (human) | GO:0005829 cytosol | CC | 65 | GO:0005829/IEA:ACCEPT; GO:0005829/TAS:ACCEPT; GO:0005829/TAS:ACCEPT; GO:0005829/TAS:ACCEPT; GO:0005829/TAS:ACCEPT; GO:0005829:CORE_FUNCTION | false | false |
| SERPINH1 (human) | GO:0005576 extracellular region | CC | 27 | GO:0031012/HDA:KEEP_AS_NON_CORE; GO:0031012/HDA:KEEP_AS_NON_CORE; GO:0031012/HDA:KEEP_AS_NON_CORE | true | false |
| SLC52A1 (human) | GO:0032217 riboflavin transmembrane transporter activity | MF | 4 | GO:0032217/IBA:ACCEPT; GO:0032217/IEA:ACCEPT; GO:0032217/IDA:ACCEPT; GO:0032217/TAS:ACCEPT; GO:0032217/IDA:ACCEPT; GO:0032217:CORE_FUNCTION | true | false |
| SLC52A1 (human) | GO:0032218 riboflavin transport | BP | 4 | GO:0032217/IBA:ACCEPT; GO:0032218/IBA:ACCEPT; GO:0032217/IEA:ACCEPT; GO:0032218/IEA:ACCEPT; GO:0032217/IDA:ACCEPT; GO:0032217/TAS:ACCEPT; GO:0032217/IDA:ACCEPT; GO:0032218/IDA:ACCEPT; GO:0032217:CORE_FUNCTION; GO:0032218:CORE_FUNCTION | true | false |
| TIMM50 (human) | GO:0004721 phosphoprotein phosphatase activity | MF | 288 | GO:0004722/IEA:KEEP_AS_NON_CORE; GO:0004721/IDA:KEEP_AS_NON_CORE; GO:0004722/IDA:KEEP_AS_NON_CORE; GO:0004725/IDA:KEEP_AS_NON_CORE | true | false |
| TPH2 (human) | GO:0042427 serotonin biosynthetic process | BP | 24 | GO:0042427/IEA:ACCEPT; GO:0042427:CORE_FUNCTION | false | false |
| UBA7 (human) | GO:0005634 nucleus | CC | 13 | GO:0005634/IEA:KEEP_AS_NON_CORE; GO:0005654/TAS:ACCEPT; GO:0005654:CORE_FUNCTION; GO:0005654:CORE_FUNCTION | true | false |
| UBA7 (human) | GO:0016567 protein ubiquitination | BP | 13 | GO:0016567/IEA:MODIFY | false | false |
| UPF3A (human) | GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | BP | 24 | NOT GO:0000184/IDA:ACCEPT | false | false |
| UPF3A (human) | GO:0003729 mRNA binding | MF | 24 | GO:0003729/IDA:ACCEPT; GO:0003729:CORE_FUNCTION | true | false |
| Drd1 (mouse) | GO:0071880 adenylate cyclase-activating adrenergic receptor signaling pathway | BP | 21 | GO:0071880/IBA:MODIFY | false | false |
| Serpinh1 (mouse) | GO:0005576 extracellular region | CC | 27 | GO:0031012/HDA:MARK_AS_OVER_ANNOTATED; GO:0031012/HDA:MARK_AS_OVER_ANNOTATED | true | false |
| Acot1 (rat) | GO:0005777 peroxisome | CC | 4 | GO:0005777/IBA:MARK_AS_OVER_ANNOTATED | false | false |
| miro-1 (worm) | GO:0007165 signal transduction | BP | 190 | GO:0097345/ISS:UNDECIDED | false | false |
| SSA1 (yeast) | GO:0042026 protein refolding | BP | 57 | GO:0042026/IBA:ACCEPT; GO:0042026/IDA:ACCEPT; GO:0042026/IDA:ACCEPT; GO:0042026:CORE_FUNCTION | true | false |
| SSA2 (yeast) | GO:0042026 protein refolding | BP | 57 | GO:0042026/IBA:ACCEPT; GO:0042026:CORE_FUNCTION | false | false |
| SSA3 (yeast) | GO:0042026 protein refolding | BP | 57 | GO:0042026/IBA:ACCEPT; GO:0042026:CORE_FUNCTION | false | false |
| SSA4 (yeast) | GO:0042026 protein refolding | BP | 57 | GO:0042026/IBA:ACCEPT; GO:0042026:CORE_FUNCTION | false | false |
| SSB1 (yeast) | GO:0042026 protein refolding | BP | 57 | GO:0042026/IBA:MODIFY | false | false |
| SSB2 (yeast) | GO:0042026 protein refolding | BP | 57 | GO:0042026/IBA:MODIFY | false | false |
| SSZ1 (yeast) | GO:0042026 protein refolding | BP | 57 | GO:0042026/IBA:MODIFY | false | false |