Homology Propagation Statistics
Generated 2026-09-26 by just propagation-stats from the cached GOA
files under genes/ (donor cache refreshed 2026-09-26).
Counts cover every gene with a cached GOA file. The unit is one annotation
(gene, term, evidence, reference, negation): pipelines that emit one GOA line
per donor, or split one annotation across qualifiers, are merged
(35,045 GOA lines → 34,265 annotations).
Reviewed annotations are those matched to an existing_annotations entry
with a final review action.
These numbers are regenerated; do not copy them into project prose.
Browse the rows in the propagation browser.
All propagation methods
| Method |
Annotations |
Reviewed |
ACCEPT |
KEEP_AS_NON_CORE |
MARK_AS_OVER_ANNOTATED |
MODIFY |
REMOVE |
UNDECIDED |
REMOVE/OVER/MODIFY |
| IBA · PAINT phylogenetic (IBA) |
11069 |
11057 |
8101 |
1753 |
327 |
461 |
198 |
217 |
9% |
| IEA · Ensembl Compara (IEA) |
8462 |
8462 |
2587 |
3995 |
1115 |
231 |
310 |
224 |
20% |
| ISS · Manual ortholog transfer |
5260 |
5260 |
2368 |
2286 |
323 |
123 |
89 |
71 |
10% |
| IEA · Combined IEA (orthology component) |
3638 |
3638 |
2700 |
615 |
135 |
139 |
23 |
26 |
8% |
| ISO · Alliance human→mouse ISO |
2009 |
2009 |
723 |
972 |
177 |
44 |
78 |
15 |
15% |
| ISO · Alliance mouse↔rat ISO |
1072 |
1072 |
296 |
590 |
122 |
29 |
26 |
9 |
17% |
| IEA · TreeGrafter (IEA) |
969 |
969 |
435 |
202 |
102 |
67 |
105 |
58 |
28% |
| ISO · RGD ISO from other mammals |
906 |
906 |
268 |
423 |
119 |
27 |
60 |
9 |
23% |
| ISS · Paper-referenced ISS |
525 |
525 |
278 |
152 |
24 |
51 |
13 |
7 |
17% |
| ISO · Paper-referenced ISO |
149 |
149 |
81 |
47 |
12 |
2 |
6 |
1 |
13% |
| ISA · TFClass DbTF classification |
89 |
89 |
88 |
0 |
0 |
1 |
0 |
0 |
1% |
| ISO · Manual ortholog transfer |
49 |
49 |
36 |
8 |
1 |
1 |
2 |
1 |
8% |
| ISO · MGI curated orthology |
39 |
39 |
16 |
16 |
0 |
3 |
4 |
0 |
18% |
| ISS · Manual complex transfer |
13 |
13 |
12 |
1 |
0 |
0 |
0 |
0 |
0% |
| ISA · Paper-referenced ISA |
8 |
8 |
6 |
1 |
1 |
0 |
0 |
0 |
12% |
| ISO · Manual complex transfer |
8 |
8 |
7 |
0 |
0 |
1 |
0 |
0 |
12% |
ISO: donor species → target species
| Donor → target |
Annotations |
Reviewed |
ACCEPT |
KEEP_AS_NON_CORE |
MARK_AS_OVER_ANNOTATED |
MODIFY |
REMOVE |
UNDECIDED |
REMOVE/OVER/MODIFY |
| Homo sapiens → Mus musculus |
2153 |
2153 |
791 |
1021 |
189 |
49 |
87 |
16 |
15% |
| Rattus norvegicus → Mus musculus |
1090 |
1090 |
302 |
602 |
122 |
29 |
26 |
9 |
16% |
| Homo sapiens → Rattus norvegicus |
454 |
454 |
128 |
234 |
71 |
8 |
9 |
4 |
19% |
| Mus musculus → Rattus norvegicus |
300 |
300 |
52 |
139 |
41 |
12 |
51 |
5 |
35% |
| Homo sapiens + Mus musculus → Rattus norvegicus |
124 |
124 |
76 |
37 |
5 |
6 |
0 |
0 |
9% |
| Saccharomyces cerevisiae → Schizosaccharomyces pombe |
51 |
51 |
38 |
9 |
1 |
1 |
1 |
1 |
6% |
| Homo sapiens + Mus musculus + Sus scrofa → Rattus norvegicus |
9 |
9 |
6 |
3 |
0 |
0 |
0 |
0 |
0% |
| unresolved → Homo sapiens |
8 |
8 |
7 |
0 |
0 |
1 |
0 |
0 |
12% |
| Homo sapiens + Sus scrofa → Rattus norvegicus |
7 |
7 |
4 |
3 |
0 |
0 |
0 |
0 |
0% |
| Canis lupus familiaris + Homo sapiens + Mus musculus → Rattus norvegicus |
5 |
5 |
4 |
0 |
0 |
1 |
0 |
0 |
20% |
| Sus scrofa → Rattus norvegicus |
5 |
5 |
0 |
4 |
1 |
0 |
0 |
0 |
20% |
| Homo sapiens → Schizosaccharomyces pombe |
4 |
4 |
3 |
0 |
0 |
0 |
1 |
0 |
25% |
| Canis lupus familiaris + Homo sapiens + Sus scrofa → Rattus norvegicus |
3 |
3 |
2 |
1 |
0 |
0 |
0 |
0 |
0% |
| Bos taurus → Mus musculus |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0% |
| Chinchilla lanigera → Rattus norvegicus |
2 |
2 |
0 |
2 |
0 |
0 |
0 |
0 |
0% |
| Cricetulus griseus → Mus musculus |
2 |
2 |
1 |
0 |
0 |
0 |
1 |
0 |
50% |
| Gallus gallus → Mus musculus |
2 |
2 |
1 |
1 |
0 |
0 |
0 |
0 |
0% |
| Pyrococcus furiosus → Schizosaccharomyces pombe |
2 |
2 |
2 |
0 |
0 |
0 |
0 |
0 |
0% |
| Aspergillus niger → Schizosaccharomyces pombe |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0% |
| Canis lupus familiaris + Homo sapiens + Mus musculus + Sus scrofa → Rattus norvegicus |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0% |
| Canis lupus familiaris + Mus musculus → Rattus norvegicus |
1 |
1 |
0 |
0 |
1 |
0 |
0 |
0 |
100% |
| Escherichia coli → Schizosaccharomyces pombe |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0% |
| Mus musculus + Sus scrofa → Rattus norvegicus |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0% |
| Mus musculus → Schizosaccharomyces pombe |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0% |
| Saccharomyces cerevisiae → Homo sapiens |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0% |
| Salmonella typhimurium → Escherichia coli |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0% |
| Xenopus laevis → Mus musculus |
1 |
1 |
1 |
0 |
0 |
0 |
0 |
0 |
0% |
ISO: does the donor still carry the term?
Donor support is the donor's current evidence for the exact transferred term
(QuickGO). INFERRED_ONLY means the donor itself only has inferred support —
typically a transfer of a transfer. ABSENT means the donor was checked and no
longer carries the term.
| Donor support |
Annotations |
Reviewed |
ACCEPT |
KEEP_AS_NON_CORE |
MARK_AS_OVER_ANNOTATED |
MODIFY |
REMOVE |
UNDECIDED |
REMOVE/OVER/MODIFY |
| EXPERIMENTAL |
3780 |
3780 |
1288 |
1845 |
387 |
93 |
140 |
27 |
16% |
| INFERRED_ONLY |
54 |
54 |
28 |
16 |
2 |
2 |
6 |
0 |
19% |
| ABSENT |
383 |
383 |
104 |
189 |
41 |
11 |
30 |
8 |
21% |
| NOT_CHECKED |
15 |
15 |
7 |
6 |
1 |
1 |
0 |
0 |
13% |
ISO: donor symbol vs target symbol
A different donor symbol flags paralog or multi-locus sourcing (for example rat
Calm1/Calm2 as donors for mouse Calm3). MIXED means the annotation has both a
namesake donor and a differently named one. It prompts a check; it is not a verdict.
| Symbol match |
Annotations |
Reviewed |
ACCEPT |
KEEP_AS_NON_CORE |
MARK_AS_OVER_ANNOTATED |
MODIFY |
REMOVE |
UNDECIDED |
REMOVE/OVER/MODIFY |
| SAME_SYMBOL |
4014 |
4014 |
1360 |
1992 |
405 |
98 |
127 |
32 |
16% |
| MIXED |
45 |
45 |
9 |
31 |
5 |
0 |
0 |
0 |
11% |
| DIFFERENT_SYMBOL |
162 |
162 |
50 |
31 |
21 |
8 |
49 |
3 |
48% |
| UNRESOLVED |
11 |
11 |
8 |
2 |
0 |
1 |
0 |
0 |
9% |
What does ISO add on top of IBA?
For each ISO annotation, the closest IBA annotation on the same target (GO is_a/part_of
closure). Annotations in the first two buckets are already implied by PAINT; the last two
are what ISO contributes beyond IBA.
| IBA on target |
biological_process |
cellular_component |
molecular_function |
All ISO |
Share |
| IBA to the same term |
190 |
197 |
199 |
586 |
14% |
| IBA to a more specific term (already entails the ISO annotation) |
95 |
81 |
88 |
264 |
6% |
| IBA only to a more general term (ISO adds specificity) |
144 |
174 |
64 |
382 |
9% |
| No related IBA (ISO adds a new assertion) |
1825 |
552 |
623 |
3000 |
71% |
Review outcome by IBA coverage (reviewed ISO annotations):
| IBA on target |
Annotations |
Reviewed |
ACCEPT |
KEEP_AS_NON_CORE |
MARK_AS_OVER_ANNOTATED |
MODIFY |
REMOVE |
UNDECIDED |
REMOVE/OVER/MODIFY |
| SAME |
586 |
586 |
460 |
100 |
10 |
7 |
8 |
1 |
4% |
| MORE_SPECIFIC |
264 |
264 |
136 |
73 |
20 |
33 |
2 |
0 |
21% |
| MORE_GENERAL |
382 |
382 |
153 |
193 |
23 |
9 |
4 |
0 |
9% |
| NONE |
3000 |
3000 |
678 |
1690 |
378 |
58 |
162 |
34 |
20% |
ISO annotations not implied by IBA, split by the target's own experimental evidence:
| Experimental on target |
Annotations |
Reviewed |
ACCEPT |
KEEP_AS_NON_CORE |
MARK_AS_OVER_ANNOTATED |
MODIFY |
REMOVE |
UNDECIDED |
REMOVE/OVER/MODIFY |
| SAME |
445 |
445 |
213 |
198 |
18 |
12 |
3 |
1 |
7% |
| MORE_SPECIFIC |
121 |
121 |
36 |
51 |
14 |
11 |
9 |
0 |
28% |
| MORE_GENERAL |
742 |
742 |
201 |
441 |
62 |
11 |
22 |
5 |
13% |
| NONE |
2074 |
2074 |
381 |
1193 |
307 |
33 |
132 |
28 |
23% |
Recorded propagation reviews
Structured review.propagation_review classifications (all methods).
| Root cause |
Annotations |
| NO_FAILURE_CORE |
934 |
| NO_FAILURE_NON_CORE |
590 |
| PROPAGATION_BAD |
433 |
| TERM_SCOPING_PROBLEM |
407 |
| UNRESOLVED |
208 |
| SOURCE_WEAK_OR_INFERRED |
65 |
| SOURCE_BAD |
43 |
| SOURCE_STALE_OR_MISSING |
27 |
| EVIDENCE_CIRCULAR_OR_REDUNDANT |
23 |
| Failure mode |
Annotations |
| GRANULARITY_MISMATCH |
329 |
| CONTEXT_OR_TISSUE_MISMATCH |
257 |
| FUNCTIONAL_DIVERGENCE |
170 |
| ROLE_CONFLATION |
169 |
| COMPARTMENT_OR_COMPLEX_MISMATCH |
139 |
| WRONG_ORTHOLOG_OR_PARALOG |
118 |
| SOURCE_EVIDENCE_WEAK |
92 |
| PSEUDO_OR_SUBACTIVITY_LOSS |
50 |
| LINEAGE_OR_TAXON_MISMATCH |
21 |
| CIRCULAR_PROPAGATION |
21 |
| SOURCE_MISCITATION |
18 |
| REGULATORY_SIGN_INVERSION |
13 |
Donor coverage
21,063 of 22,227 donor-based annotations have at least one donor checked.