AFF1 (P51825) annotation-provenance analysis

Computed by analyze_aff1_annotations.py. Every number below is derived by that script from the GOA TSV, UniProt, QuickGO and IntAct; none is hand-entered. Re-run to reproduce.

A. WITH/FROM resolution

token rows kind resolves to status note
ARBA:ARBA00026330 6 signature_or_rule – – an automatic-pipeline source, not a protein
FB:FBgn0041111 1,2,4,5 protein Q9VQI9 AFFL_DROME (lilli, Drosophila melanogaster) Swiss-Prot 3 candidate entries
InterPro:IPR007797 7 signature_or_rule – – an automatic-pipeline source, not a protein
InterPro:IPR043640 6 signature_or_rule – – an automatic-pipeline source, not a protein
MGI:MGI:106927 1 protein P51827 AFF3_MOUSE (Aff3, Mus musculus) Swiss-Prot 4 candidate entries
MGI:MGI:1100819 1 protein O88573 AFF1_MOUSE (Aff1, Mus musculus) Swiss-Prot 10 candidate entries
MGI:MGI:1202294 4 protein O55112 AFF2_MOUSE (Aff2, Mus musculus) Swiss-Prot 3 candidate entries
PANTHER:PTN000829417 1,2,3,4,5 panther_node – – an internal PANTHER tree node, not a protein
UniProtKB-SubCell:SL-0191 6 signature_or_rule – – an automatic-pipeline source, not a protein
UniProtKB:P04608 9 protein P04608 TAT_HV1H2 (tat, Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Swiss-Prot
UniProtKB:P42568 8,10 protein P42568 AF9_HUMAN (MLLT3, Homo sapiens) Swiss-Prot
UniProtKB:P51825 1,3 protein P51825 AFF1_HUMAN (AFF1, Homo sapiens) Swiss-Prot self-reference: the subject itself

B. Donor evidence for the propagated term

For each (donor, propagated term) pair: what does the donor itself hold? "The source only carries the same family-level inference" is a testable claim, and IBA WITH/FROM lists experimentally-annotated members by construction, so it is usually false.

donor propagated term donor annotations donor evidence codes holds the exact term own experimental evidence
O55112 Aff2 (Mus musculus) GO:0050877 2 IBA×1, IMP×1 yes yes
O88573 Aff1 (Mus musculus) GO:0006355 5 IBA×1, IDA×1, ISO×2, TAS×1 yes yes
P51825 AFF1 (Homo sapiens) GO:0006354 2 EXP×1, IBA×1 yes yes
P51825 AFF1 (Homo sapiens) GO:0006355 3 IBA×1, IMP×2 yes yes
P51827 Aff3 (Mus musculus) GO:0006355 6 IBA×1, IDA×2, IMP×2, TAS×1 yes yes
Q9VQI9 lilli (Drosophila melanogaster) GO:0003712 2 IBA×1, IMP×1 yes yes
Q9VQI9 lilli (Drosophila melanogaster) GO:0006355 5 IBA×1, IGI×1, IMP×2, NAS×1 yes yes
Q9VQI9 lilli (Drosophila melanogaster) GO:0032783 3 IBA×1, IPI×1, NAS×1 yes yes
Q9VQI9 lilli (Drosophila melanogaster) GO:0050877 2 IBA×1, IMP×1 yes yes

C. Reference-projection test

How many distinct gene products does each cited reference annotate, and does the functional term spread across the set or stay on the perturbed gene? Entity counts are distinct id sets, not annotation totals.

reference annotations distinct entities verdict
PMID:20159561 1 1 single-entity: no projection
PMID:21729782 26 17 17 entities – inspect per-term spread
PMID:22190034 183 104 104 entities – inspect per-term spread
PMID:22195968 61 26 26 entities – inspect per-term spread
PMID:22547686 1 1 single-entity: no projection
PMID:23260655 8 4 4 entities – inspect per-term spread
PMID:41062835 8 2 2 entities – inspect per-term spread

PMID:21729782: 17 entities

term entities
GO:0005515 None 17: UniProtKB:A0JLT2, UniProtKB:O00472, UniProtKB:O43513, UniProtKB:O60563, UniProtKB:O60583, UniProtKB:O95402, UniProtKB:P42568, UniProtKB:P50750, UniProtKB:P51825, UniProtKB:P55199, UniProtKB:Q03111, UniProtKB:Q659A1 …

PMID:22190034: 104 entities

term entities
GO:0005515 None 104: UniProtKB:O00303, UniProtKB:O14734, UniProtKB:O14929, UniProtKB:O15355, UniProtKB:O15371, UniProtKB:O15372, UniProtKB:O15379, UniProtKB:O43324, UniProtKB:O43865, UniProtKB:O60232, UniProtKB:O60518, UniProtKB:O60563 …

PMID:22195968: 26 entities

term entities
GO:0000791 None 4: UniProtKB:Q659A1, UniProtKB:Q9ESC8, UniProtKB:Q9VQI9, UniProtKB:Q9Y2F5
GO:0003682 None 2: UniProtKB:Q9VW51, UniProtKB:Q9W1R4
GO:0005515 None 3: UniProtKB:P55199, UniProtKB:Q659A1, UniProtKB:Q9Y2F5
GO:0005634 None 3: UniProtKB:Q9ESC8, UniProtKB:Q9VW51, UniProtKB:Q9Y2F5
GO:0005694 None 1: UniProtKB:Q9ESC8
GO:0008023 None 17: UniProtKB:O00472, UniProtKB:O96433, UniProtKB:P42568, UniProtKB:P50750, UniProtKB:P51825, UniProtKB:P55199, UniProtKB:Q03111, UniProtKB:Q659A1, UniProtKB:Q7JRJ1, UniProtKB:Q8SZZ8, UniProtKB:Q96CJ1, UniProtKB:Q96JC9 …
GO:0015030 None 2: UniProtKB:P55199, UniProtKB:Q9Y2F5
GO:0032783 None 10: UniProtKB:A0A0B4KG69, UniProtKB:A1Z7L5, UniProtKB:A1Z7L6, UniProtKB:O17432, UniProtKB:O96433, UniProtKB:Q7JRJ1, UniProtKB:Q8SZZ8, UniProtKB:Q9VF92, UniProtKB:Q9VQI9, UniProtKB:Q9W1R4
GO:0042795 None 7: UniProtKB:O00472, UniProtKB:O08856, UniProtKB:P55199, UniProtKB:Q9HB65, UniProtKB:Q9VW51, UniProtKB:Q9W1R4, UniProtKB:Q9Y2F5
GO:1905382 None 5: ComplexPortal:CPX-2710, UniProtKB:Q7JRJ1, UniProtKB:Q8SZZ8, UniProtKB:Q9VW51, UniProtKB:Q9W1R4

PMID:23260655: 4 entities

term entities
GO:0005515 None 4: UniProtKB:P42568, UniProtKB:P51825, UniProtKB:Q8TEK3, UniProtKB:Q9HC52
GO:0060090 None 1: UniProtKB:P42568

PMID:41062835: 2 entities

term entities
GO:0000785 None 1: UniProtKB:P51825
GO:0003711 None 1: UniProtKB:P51825
GO:0005634 None 1: UniProtKB:P51825
GO:0006974 None 1: UniProtKB:P51825
GO:0032786 None 1: UniProtKB:P51825
GO:0032968 None 1: UniProtKB:P51825
GO:0090734 None 2: UniProtKB:P09874, UniProtKB:P51825

D. Term relations (fetched, not inferred from labels)

claim expected observed agrees why the review needs it
is GO:0008023 an ancestor of GO:0032783? True True yes SEC is a kind of transcription elongation factor complex, so the GO:0008023 IDA is the less precise of the two complex rows
is GO:0032786 an ancestor of GO:0032968? True True yes the Pol II elongation-activation term is a child of the generic one, so the two IMP rows from one reference are parent+child, not independent
is GO:0006355 an ancestor of GO:0032786? True True yes positive regulation of elongation sits under regulation of DNA-templated transcription, so the IBA GO:0006355 row is an ancestor of what the human IMP rows already assert
is GO:0010468 an ancestor of GO:0006355? True True yes regulation of DNA-templated transcription is under regulation of gene expression, so the InterPro2GO GO:0010468 row is the least specific of the regulation rows
is GO:0003712 an ancestor of GO:0003711? False False yes transcription elongation factor activity is NOT under transcription coregulator activity -- the two MF rows are different claims, not a general/specific pair
is GO:0005634 an ancestor of GO:0000785? False False yes chromatin is not part_of nucleus in GO's is_a/part_of closure, so the chromatin and nucleus rows are separate location claims
is GO:0000785 an ancestor of GO:0090734? False False yes site of DNA damage is not under chromatin, so the two damage-associated location rows are not a general/specific pair
is GO:0006355 an ancestor of GO:0032968? True True yes raised by the PR reviewer: GO:0006355 is an ancestor of GO:0032968, so listing both in one core_function's directly_involved_in is redundant by the same logic used to collapse GO:0032786 onto GO:0032968 in the rows
is GO:0006355 an ancestor of GO:0045668? False False yes the osteoblast-differentiation term is NOT under regulation of DNA-templated transcription, so core function 3 may legitimately carry both

E. PANTHER node reach

Node PANTHER:PTN000829417 carries 395 IBA annotations over 79 recipient gene products.

term recipients human recipients under this node
GO:0003712 79 4: AFF2, AFF1, AFF3, AFF4
GO:0006354 79 4: AFF2, AFF1, AFF3, AFF4
GO:0006355 79 4: AFF2, AFF1, AFF3, AFF4
GO:0032783 79 4: AFF2, AFF1, AFF3, AFF4
GO:0050877 79 4: AFF2, AFF1, AFF3, AFF4

Full recipient lists are in results.json under node_reach.terms_on_node; only the count and the human members are shown here (nothing is filtered from the stored data).

Reciprocally, which PANTHER nodes give each term to a human gene product. Only nodes reaching AFF-family members are tabulated; the complete node lists, including the many unrelated nodes that supply the generic terms to other families, are in results.json under node_reach.human_iba_holders_by_term.

term total human IBA rows nodes reaching an AFF gene AFF recipients
GO:0003712 81 PANTHER:PTN000829417 (44 nodes total) AFF2, AFF1, AFF3, AFF4
GO:0006354 6 PANTHER:PTN000829417 (2 nodes total) AFF2, AFF1, AFF3, AFF4
GO:0006355 192 PANTHER:PTN000829417 (60 nodes total) AFF2, AFF1, AFF3, AFF4
GO:0032783 4 PANTHER:PTN000829417 (2 nodes total) AFF2, AFF1, AFF3, AFF4
GO:0032783 4 PANTHER:PTN002575678 (2 nodes total) AFF2
GO:0050877 4 PANTHER:PTN000829417 (1 nodes total) AFF2, AFF1, AFF3, AFF4

H. Is the true ortholog among the donors?

A paralog donor set is legitimate for IBA, but it means no ortholog-strength inference is available on that row. Mouse Aff1 (O88573) is AFF1's 1:1 ortholog.

term donors ortholog cited? ortholog's own annotations in that subtree
GO:0003712 Q9VQI9 fly lilli no 1 (IBA×1)
GO:0006354 P51825 AFF1 no 1 (IBA×1)
GO:0006355 Q9VQI9 fly lilli, P51827 mouse Aff3, O88573 mouse Aff1, P51825 AFF1 yes 5 (IBA×1, IDA×1, ISO×2, TAS×1)
GO:0032783 Q9VQI9 fly lilli no 2 (IBA×1, ISO×1)
GO:0050877 Q9VQI9 fly lilli, O55112 mouse Aff2 no 1 (IBA×1)

I. One reference, two levels of precision, split by clade

PMID:22195968 annotates both GO:0008023 and the more specific GO:0032783. Resolving every recipient's organism shows which clade got which term.

recipient organism / gene got the specific term?
UniProtKB:A0A0B4KG69 Drosophila melanogaster / ear yes
UniProtKB:A1Z7L5 Drosophila melanogaster / Uspl1l yes
UniProtKB:A1Z7L6 Drosophila melanogaster / Dmel\CG8229 yes
UniProtKB:O00472 Homo sapiens / ELL2 no
UniProtKB:O17432 Drosophila melanogaster / Cdk9 yes
UniProtKB:O96433 Drosophila melanogaster / CycT yes
UniProtKB:P42568 Homo sapiens / MLLT3 no
UniProtKB:P50750 Homo sapiens / CDK9 no
UniProtKB:P51825 Homo sapiens / AFF1 no
UniProtKB:P55199 Homo sapiens / ELL no
UniProtKB:Q03111 Homo sapiens / MLLT1 no
UniProtKB:Q659A1 Homo sapiens / ICE2 no
UniProtKB:Q7JRJ1 Drosophila melanogaster / Eaf yes
UniProtKB:Q8SZZ8 Drosophila melanogaster / Ice2 yes
UniProtKB:Q96CJ1 Homo sapiens / EAF2 no
UniProtKB:Q96JC9 Homo sapiens / EAF1 no
UniProtKB:Q9HB65 Homo sapiens / ELL3 no
UniProtKB:Q9UHB7 Homo sapiens / AFF4 no
UniProtKB:Q9VF92 Drosophila melanogaster / ear yes
UniProtKB:Q9VQI9 Drosophila melanogaster / lilli yes
UniProtKB:Q9VW51 Drosophila melanogaster / Ell no
UniProtKB:Q9W1R4 Drosophila melanogaster / Ice1 yes

F. IntAct records expanded per partner

NbExp is not an experiment count -- it has been observed counting sub-methods of one screen, replicates, and even a partner's domains. Distinct publications and distinct detection methods are counted here.

All 104 IntAct records are accounted for: 102 protein records over 43 partner entities, plus 2 records in which the subject appears as its own Ensembl transcript paired with an RNAcentral ncRNA (an RNA-RNA record, not a protein interaction of AFF1). The run fails if any record is unassigned; a predicate that silently drops records yields a wrong partner set even when the count looks plausible.

Partner entities that are not proteins (a gene id, a fusion construct): EBI-2620048, EBI-2620068, EBI-2620075, ENSG00000136997.

Partners supported by two or more distinct PMIDs: O00472, P42568, P48426, P50750, Q03111, Q96JC9, Q9HB65, Q9UHB7.

partner name records distinct PMIDs all pub. ids distinct methods max MI subject form
P50750 CDK9 16 7 16 5 0.9 P51825
Q96JC9 EAF1 5 3 8 1 0.64 P51825
Q9HB65 ELL3 4 3 8 1 0.64 P51825
Q03111 MLLT1 9 2 5 3 0.6 P51825
Q9UHB7 AFF4 8 2 4 3 0.6 P51825
P42568 MLLT3 7 2 5 5 0.73 P51825
O00472 ELL2 2 2 7 1 0.53 P51825
P48426 PIP4K2A 2 2 6 1 0.53 P51825
O60563 CCNT1 8 1 2 3 0.53 P51825
P53367 ARFIP1 3 1 2 3 0.56 P51825-3 (isoform only)
P04608 tat 3 1 3 2 0.56 P51825
Q9ERL0 Mllt1 2 1 5 1 0.35 P51825
Q03164-PRO_0000390949 Q03164-PRO_0000390949 2 1 2 1 0.35 P51825
O95402 MED26 2 1 2 1 0.35 P51825
Q2Q440 q2q440_human 1 1 2 1 0.35 P51825
Q8TD98 q8td98_human 1 1 2 1 0.35 P51825
EBI-2620048 mll_aff4_fusion 1 1 2 1 0.35 P51825
EBI-2620068 mll_enl_human_protein 1 1 2 1 0.35 P51825
EBI-2620075 mll_aff4_fusion-1 1 1 2 1 0.4 P51825
Q5NEM9 q5nem9_fratt 1 1 2 1 0.37 P51825
A0A2U2GVV5 a0a2u2gvv5_yerpe 1 1 2 1 0.37 P51825
ENSG00000136997 myc_human_gene 1 1 2 1 0.35 P51825
Q8NCB2-2 CAMKV 1 1 3 1 0.35 P51825
Q9DCX1 Mad2l1bp 1 1 5 1 0.35 P51825
A2AM29 Mllt3 1 1 3 1 0.44 P51825
P50750-2 CDK9 1 1 3 1 0.35 P51825
Q8NCB2 CAMKV 1 1 3 1 0.35 P51825
Q99PL5 Rrbp1 1 1 5 1 0.35 P51825
Q8TF50 ZNF526 1 1 5 1 0.35 P51825
Q8VE37 Rcc1 1 1 5 1 0.35 P51825
Q8N3E9 PLCD3 1 1 3 1 0.35 P51825
P61328 FGF12 1 1 3 1 0.35 P51825
O95218 ZRANB2 1 1 2 1 0.27 P51825
O15198 SMAD9 1 1 5 1 0.37 P51825
O15403 SLC16A6 1 1 5 1 0.35 P51825
P52815 MRPL12 1 1 3 1 0.4 P51825
Q96T37 RBM15 1 1 2 1 0.27 P51825
Q9Y3A5 SBDS 1 1 2 1 0.27 P51825
Q9H4G0 EPB41L1 1 1 3 1 0.35 P51825
P12883 MYH7 1 1 5 1 0.35 P51825
Q9Y2J2 EPB41L3 1 1 3 1 0.35 P51825
Q13547 HDAC1 1 1 5 1 0.35 P51825
P06748 NPM1 1 1 2 1 0.27 P51825

J. Disorder coverage (computed from the UniProt feature table)

4 Disordered REGION features cover 901 of 1210 residues (74.5%): 1-45, 73-314, 366-957, 1098-1119. Derived rather than asserted, because a first draft of the review rounded this to "about a thousand", overstating it by ~11%.

G. affinage recall against the GOA reference set

gates_passed: True is a statement about precision -- that the citations returned are real and correctly quoted. It carries no recall guarantee, and the number above is what recall actually was on the reference set that decides this gene's annotations.