ARBA rule redundancy and generic rules
Generated by rule_redundancy.py; do not edit by hand. Per-rule measures for every
GO-asserting rule are in rule_redundancy.tsv.
Redundancy across all ARBA GO rules
- ARBA GO rules: 12936, each asserting one term, with 232979 condition sets.
- GO terms asserted by more than one rule: 0 of 12936, covering 0 rules.
- Rules that share a signature with another rule asserting the same term: 0.
- Condition sets duplicated exactly in another rule for the same term: 0.
- Condition sets covered by a rule asserting a more specific term: 145142 (62%); rules covered in every set: 2678.
- Reviewed genes that carry both an ARBA term and an ARBA descendant of it: 6 of 2411. UniProt keeps the most specific ARBA term, so generic and specific ARBA rules do not stack on a protein; a covered condition set is dead weight rather than a source of extra annotations.
Do covered rules produce annotations?
QuickGO annotation counts for seeded random samples (seed 7, up to 60 rules each):
| sample | rules sampled | with no annotations | median annotations |
|---|---|---|---|
| fully covered | 60 | 57 (95%) | 0 |
| partly covered | 60 | 11 (18%) | 392 |
| all GO rules | 60 | 19 (32%) | 157 |
Generic rules seen in gene reviews
Rules whose term has more than 200 GO descendants and that produced at least 10 annotations in our gene reviews (36 rules). Covered is the share of the rule's condition sets that a more specific rule also matches. Descendant present is the share of the rule's reviewed annotations where the gene already has a more specific term, from any source (and from ARBA). Kept and rejected are the reviews' actions on the rule's rows.
| rule | term | annotations (human) | sets | covered | rows | descendant present: any (ARBA) | kept | modified | rejected |
|---|---|---|---|---|---|---|---|---|---|
| ARBA00026971 | cytoplasm | 2,676,145 (7,245) | 2388 | 22% | 155 | 80% (0%) | 72% | 12% | 15% |
| ARBA00027533 | catalytic activity | 776,816 (133) | 2875 | 82% | 39 | 95% (0%) | 13% | 54% | 33% |
| ARBA00028902 | protein-containing complex | 115,456 (695) | 886 | 62% | 35 | 86% (0%) | 26% | 37% | 31% |
| ARBA00028763 | membrane | 955,700 (2,028) | 1269 | 65% | 46 | 98% (0%) | 54% | 13% | 33% |
| ARBA00027702 | system development | 144,416 (403) | 450 | 45% | 29 | 93% (0%) | 34% | 17% | 48% |
| ARBA00029247 | animal organ development | 97,974 (492) | 245 | 22% | 32 | 94% (0%) | 47% | 9% | 44% |
| ARBA00028334 | regulation of gene expression | 185,510 (848) | 932 | 70% | 38 | 95% (0%) | 55% | 24% | 21% |
| ARBA00029050 | signal transduction | 156,728 (389) | 630 | 62% | 29 | 90% (0%) | 55% | 31% | 14% |
| ARBA00026300 | response to stress | 166,446 (414) | 707 | 63% | 33 | 91% (0%) | 61% | 9% | 27% |
| ARBA00028953 | endomembrane system | 201,739 (902) | 533 | 60% | 30 | 97% (0%) | 63% | 17% | 20% |
| ARBA00026583 | anatomical structure morphogenesis | 96,151 (172) | 291 | 33% | 29 | 97% (0%) | 62% | 3% | 34% |
| ARBA00028747 | oxidoreductase activity | 407,599 (208) | 582 | 47% | 15 | 100% (0%) | 27% | 13% | 60% |
| ARBA00027126 | regulation of intracellular signal transduction | 10,667 (131) | 189 | 66% | 13 | 100% (0%) | 23% | 23% | 54% |
| ARBA00028689 | regulation of developmental process | 31,579 (144) | 248 | 50% | 24 | 96% (0%) | 62% | 12% | 25% |
| ARBA00028665 | cell development | 38,374 (136) | 174 | 44% | 14 | 100% (0%) | 43% | 0% | 57% |
| ARBA00028859 | regulation of multicellular organismal process | 32,726 (228) | 296 | 57% | 14 | 100% (0%) | 43% | 0% | 57% |
| ARBA00027429 | cell differentiation | 78,238 (318) | 299 | 44% | 26 | 85% (0%) | 69% | 12% | 15% |
| ARBA00028591 | lipid metabolic process | 36,756 (130) | 366 | 66% | 11 | 82% (0%) | 36% | 9% | 55% |
| ARBA00028065 | tissue development | 30,924 (134) | 178 | 19% | 13 | 92% (0%) | 46% | 23% | 31% |
| ARBA00027483 | cellular response to oxygen-containing compound | 10,300 (86) | 132 | 28% | 11 | 91% (0%) | 27% | 0% | 64% |
| ARBA00028945 | cell communication | 33,985 (240) | 670 | 90% | 10 | 100% (0%) | 40% | 50% | 10% |
| ARBA00028442 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | 359,441 (198) | 122 | 21% | 11 | 100% (0%) | 45% | 36% | 18% |
| ARBA00028184 | cellular response to stress | 25,285 (209) | 336 | 65% | 13 | 100% (0%) | 54% | 15% | 31% |
| ARBA00028891 | positive regulation of multicellular organismal process | 22,005 (220) | 136 | 35% | 11 | 91% (0%) | 45% | 9% | 45% |
| ARBA00029007 | post-embryonic development | 33,943 (1) | 111 | 18% | 13 | 62% (0%) | 54% | 8% | 38% |
| ARBA00029053 | cell surface receptor signaling pathway | 22,471 (323) | 232 | 50% | 10 | 90% (0%) | 50% | 20% | 30% |
| ARBA00028036 | plasma membrane bounded cell projection | 30,411 (150) | 220 | 30% | 12 | 100% (0%) | 58% | 25% | 17% |
| ARBA00026330 | nucleus | 1,340,501 (5,635) | 1293 | 26% | 19 | 32% (0%) | 79% | 5% | 16% |
| ARBA00026297 | carbohydrate derivative metabolic process | 53,046 (150) | 286 | 63% | 12 | 100% (0%) | 58% | 17% | 17% |
| ARBA00028249 | vesicle-mediated transport | 69,446 (355) | 162 | 16% | 10 | 70% (0%) | 70% | 20% | 10% |
| ARBA00027801 | plasma membrane | 1,510,394 (15,871) | 686 | 11% | 21 | 43% (0%) | 81% | 5% | 5% |
| ARBA00027546 | regulation of cell population proliferation | 15,794 (133) | 116 | 7% | 14 | 93% (0%) | 86% | 7% | 7% |
| ARBA00027281 | bounding membrane of organelle | 39,834 (184) | 171 | 25% | 12 | 100% (0%) | 83% | 0% | 17% |
| ARBA00027086 | regulation of apoptotic process | 15,984 (248) | 105 | 58% | 11 | 91% (0%) | 82% | 9% | 9% |
| ARBA00026361 | chromosome | 97,871 (538) | 241 | 61% | 11 | 82% (0%) | 82% | 0% | 9% |
| ARBA00026313 | immune response | 9,205 (145) | 98 | 18% | 10 | 100% (0%) | 100% | 0% | 0% |