IRD-wide checks: seeds inside the clade, and fully re-annotated blocks
Generated by ird_seed_check.py from PAINT IBD.gaf, the PAINT leaf GAF and the PANTHER
trees. Detail rows are in the git-ignored ird_seed_in_clade.tsv and
ird_fully_reannotated.tsv.
1. The IRD clade contains a seed of the IBD it blocks
- IRD rows: 2538. Seed slots on their ancestral IBDs: 10532 (7393 distinct seeds, 7387 mapped to UniProt).
- Clade-member rows (IRD node, term, leaf) checked: 52660 of 52660 (only leaves with a UniProt accession can match a seed).
- Not mapped: 3 JaponicusDB seeds (UniProt ID mapping rejected source JaponicusDB: {'url': 'http://rest.uniprot.org/idmapping/run', 'messages': ["The param).
- 144 IRD rows (5.7%) have at least one seed of the blocked IBD inside their own clade, in 113 families.
Such an IRD denies the function to a protein whose own experiment was used to infer
it. That is not always an error (the seed's annotation may be weak, or PAINT may judge
it a lineage-specific gain), but each one should be checked first.
Families with the most such rows:
| Family | IRD rows with a seed in the clade |
|---|---|
| PTHR11937 | 4 |
| PTHR10625 | 3 |
| PTHR11207 | 3 |
| PTHR11588 | 3 |
| PTHR13723 | 3 |
| PTHR20275 | 3 |
| PTHR10353 | 2 |
| PTHR10953 | 2 |
| PTHR11256 | 2 |
| PTHR11309 | 2 |
| PTHR11394 | 2 |
| PTHR11610 | 2 |
| PTHR11778 | 2 |
| PTHR12121 | 2 |
| PTHR12483 | 2 |
2. Fully re-annotated IRD rows (20)
Every protein in the clade still gets the blocked term, or a term below it in GO (by
is_a or part_of, the relations analyze_ird.py uses), as a positive IBA. The IRD
therefore removes nothing a user can see. The source of each IBA is the PTN node in
the leaf GAF's with/from (every PTN listed there). The kinds are:
- Below (0): PAINT annotates the term again on a
node inside the IRD clade, overriding the IRD. - Same node (2): the IRD node itself carries an
IBD for a more specific term, for example a mitochondrion IBD beside a NOT cytoplasm. - Above (18): an ancestral IBD carries a more specific
term that the IRD does not block.
Only clade members with a UniProt accession can be checked; the Clade column gives
checked/all leaves. A clade where few leaves are checked is weaker evidence.
In each case the IRD contradicts annotations PAINT itself propagates: a gene cannot lack
a process or location while having one of its subtypes or parts. Either the IRD should
also block the more specific term, or it should be retracted. Some pairs cross GO
aspects through part_of (a transporter activity that is part of transmembrane
transport); those are listed but are weaker evidence of inconsistency.
| Family | IRD node | Blocked term | IRD date | Clade | Kind | IBA sources (node, term, where) |
|---|---|---|---|---|---|---|
| PTHR10131 | PTN007421972 | GO:0007166 cell surface receptor signaling pathway | 20250411 | 3/3 | above | PTN000805720 GO:0033209 (above) |
| PTHR10794 | PTN000082718 | GO:0034338 short-chain carboxylesterase activity | 20200313 | 1/1 | above | PTN000082647 GO:0008126 (above) |
| PTHR11119 | PTN002476593 | GO:0015882 L-ascorbic acid transmembrane transport | 20241120 | 1/1 | above | PTN002595861 GO:0015229 (above) |
| PTHR11610 | PTN000176957 | GO:0016042 lipid catabolic process | 20241120 | 9/9 | above | PTN000906454 GO:0019433 (above) |
| PTHR11610 | PTN000176957 | GO:0016298 lipase activity | 20260528 | 9/9 | above | PTN000906454 GO:0004465 (above); PTN000906454 GO:0008970 (above) |
| PTHR11610 | PTN008325477 | GO:0016042 lipid catabolic process | 20241120 | 12/12 | above | PTN000906454 GO:0019433 (above) |
| PTHR11610 | PTN008325477 | GO:0016298 lipase activity | 20260528 | 12/12 | above | PTN000906454 GO:0004465 (above); PTN000906454 GO:0008970 (above) |
| PTHR11958 | PTN002632768 | GO:0015813 L-glutamate transmembrane transport | 20250903 | 20/20 | above | PTN000238242 GO:0005313 (above) |
| PTHR19321 | PTN004511774 | GO:0005819 spindle | 20230603 | 1/1 | above | PTN000448590 GO:1990023 (above) |
| PTHR24056 | PTN000623365 | GO:0000307 cyclin-dependent protein kinase holoenzyme complex | 20260313 | 1/1 | above | PTN000623095 GO:1990508 (above) |
| PTHR24221 | PTN000657226 | GO:0055085 transmembrane transport | 20250903 | 10/10 | above | PTN000657189 GO:0042626 (above) |
| PTHR24221 | PTN000657241 | GO:0055085 transmembrane transport | 20250903 | 12/12 | same node | PTN000657189 GO:0042626 (above); PTN000657241 GO:0042910 (same node) |
| PTHR24221 | PTN000657258 | GO:0055085 transmembrane transport | 20250903 | 1/1 | above | PTN000657189 GO:0042626 (above) |
| PTHR24221 | PTN000657261 | GO:0055085 transmembrane transport | 20250903 | 1/1 | above | PTN000657189 GO:0042626 (above) |
| PTHR24221 | PTN001542468 | GO:0055085 transmembrane transport | 20250903 | 3/3 | above | PTN000657189 GO:0042626 (above) |
| PTHR24235 | PTN000662954 | GO:0007218 neuropeptide signaling pathway | 20250618 | 8/8 | above | PTN002538187 GO:0008188 (above) |
| PTHR33694 | PTN008658623 | GO:0005737 cytoplasm | 20260828 | 54/54 | same node | PTN008658623 GO:0005739 (same node) |
| PTHR43020 | PTN000228777 | GO:0035596 methylthiotransferase activity | 20260530 | 85/85 | above | PTN000228824 GO:0035597 (above) |
| PTHR43020 | PTN000228777 | GO:0035600 tRNA methylthiolation | 20241121 | 85/85 | above | PTN000228824 GO:0035597 (above) |
| PTHR48017 | PTN004585555 | GO:0003333 amino acid transmembrane transport | 20260828 | 31/31 | above | PTN001118955 GO:0015171 (above) |