AFF4 (Q9UHB7) annotation-provenance audit

Generated by analyze_aff4_annotations.py. Every number below is computed by that
script; nothing here is hand-entered. Re-run it and diff before trusting this file.

1. GOA row census

rows in AFF4-goa.tsv (excluding header): 43
distinct (term, evidence, reference, with/from, qualifier) tuples: 43

GO term	rows
GO:0000791	2
GO:0001650	1
GO:0003712	1
GO:0005515	15
GO:0005634	2
GO:0005654	12
GO:0005694	2
GO:0006354	1
GO:0006355	1
GO:0008023	1
GO:0010468	1
GO:0016604	1
GO:0032783	1
GO:0034976	1
GO:0050877	1

evidence	rows
EXP	2
IBA	5
IDA	4
IEA	5
IPI	15
ISS	1
TAS	11

2. WITH/FROM resolution

Every token in column 11 of the GOA table, resolved. Swiss-Prot/TrEMBL status is
printed next to every name: an unreviewed entry's protein name is an automatic
by-similarity label even when its GO annotations are experimental.

token	kind	resolved	entry	reviewed	organism	len	candidates
`ARBA:ARBA00026330`	arba_rule	-	-	-	-	-	0
`FB:FBgn0041111`	protein	Q9VQI9	AFFL_DROME (lilli)	Swiss-Prot	Drosophila melanogaster	1673	3
`InterPro:IPR007797`	interpro_signature	-	-	-	-	-	0
`InterPro:IPR043640`	interpro_signature	-	-	-	-	-	0
`MGI:MGI:106927`	protein	P51827	AFF3_MOUSE (Aff3)	Swiss-Prot	Mus musculus	1254	4
`MGI:MGI:1100819`	protein	O88573	AFF1_MOUSE (Aff1)	Swiss-Prot	Mus musculus	1216	10
`MGI:MGI:1202294`	protein	O55112	AFF2_MOUSE (Aff2)	Swiss-Prot	Mus musculus	1272	3
`PANTHER:PTN000829417`	panther_tree_node	-	-	-	-	-	0
`UniProtKB-SubCell:SL-0191`	UniProtKB-SubCell	-	-	-	-	-	0
`UniProtKB-SubCell:SL-0468`	UniProtKB-SubCell	-	-	-	-	-	0
`UniProtKB:A0A8I6GGV9`	protein	A0A8I6GGV9	A0A8I6GGV9_RAT (Aff4)	TrEMBL	Rattus norvegicus	1164	1
`UniProtKB:O60563`	protein	O60563	CCNT1_HUMAN (CCNT1)	Swiss-Prot	Homo sapiens	726	1
`UniProtKB:P04608`	protein	P04608	TAT_HV1H2 (tat)	Swiss-Prot	Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)	86	1
`UniProtKB:P42568`	protein	P42568	AF9_HUMAN (MLLT3)	Swiss-Prot	Homo sapiens	568	1
`UniProtKB:P51825`	protein	P51825	AFF1_HUMAN (AFF1)	Swiss-Prot	Homo sapiens	1210	1
`UniProtKB:P63010`	protein	P63010	AP2B1_HUMAN (AP2B1)	Swiss-Prot	Homo sapiens	937	1
`UniProtKB:Q03111`	protein	Q03111	ENL_HUMAN (MLLT1)	Swiss-Prot	Homo sapiens	559	1
`UniProtKB:Q08379`	protein	Q08379	GOGA2_HUMAN (GOLGA2)	Swiss-Prot	Homo sapiens	1002	1
`UniProtKB:Q12933`	protein	Q12933	TRAF2_HUMAN (TRAF2)	Swiss-Prot	Homo sapiens	501	1
`UniProtKB:Q5JR59`	protein	Q5JR59	MTUS2_HUMAN (MTUS2)	Swiss-Prot	Homo sapiens	1369	1
`UniProtKB:Q8IUQ4`	protein	Q8IUQ4	SIAH1_HUMAN (SIAH1)	Swiss-Prot	Homo sapiens	282	1
`UniProtKB:Q9ESC8`	protein	Q9ESC8	AFF4_MOUSE (Aff4)	Swiss-Prot	Mus musculus	1160	1
`ensembl:ENSMUSP00000051479`	ensembl	-	-	-	-	-	0
`ensembl:ENSRNOP00000088228`	ensembl	-	-	-	-	-	0

3. What each donor's OWN evidence is for the propagated term

Queried per row with goUsage=descendants (is_a,part_of), so a donor whose
experiment sits at a more specific term than the one propagated is visible.

GO:0006355 regulation of DNA-templated transcription — IBA (GO_REF:0000033)

donor token	resolved	own annotations to this term or a descendant
`FB:FBgn0041111`	AFFL_DROME (lilli)	GO:0006355 IBA GO_REF:0000033; GO:0006355 IMP PMID:11171404; GO:0034243 NAS PMID:28350987; GO:0045944 IMP PMID:28350987; GO:0045944 IGI PMID:28350987
`MGI:MGI:106927`	AFF3_MOUSE (Aff3)	GO:0003700 TAS PMID:11923441; GO:0003700 IDA PMID:25162227; GO:0003700 IMP PMID:25162227; GO:0006355 IBA GO_REF:0000033; GO:0006355 IDA PMID:25162227; GO:0006355 IMP PMID:25162227
`MGI:MGI:1100819`	AFF1_MOUSE (Aff1)	GO:0045893 IDA PMID:9365243; GO:0003700 TAS PMID:11923441; GO:0006355 IBA GO_REF:0000033; GO:0032786 ISO GO_REF:0000119; GO:0032968 ISO GO_REF:0000119
`PANTHER:PTN000829417`	panther_tree_node	n/a
`UniProtKB:P51825`	AFF1_HUMAN (AFF1)	GO:0006355 IBA GO_REF:0000033; GO:0032786 IMP PMID:41062835; GO:0032968 IMP PMID:41062835

GO:0003712 transcription coregulator activity — IBA (GO_REF:0000033)

donor token	resolved	own annotations to this term or a descendant
`FB:FBgn0041111`	AFFL_DROME (lilli)	GO:0003712 IBA GO_REF:0000033; GO:0003712 IMP PMID:11171404
`PANTHER:PTN000829417`	panther_tree_node	n/a

GO:0006354 DNA-templated transcription elongation — IBA (GO_REF:0000033)

donor token	resolved	own annotations to this term or a descendant
`PANTHER:PTN000829417`	panther_tree_node	n/a
`UniProtKB:P51825`	AFF1_HUMAN (AFF1)	GO:0006354 IBA GO_REF:0000033; GO:0006354 EXP PMID:22547686

GO:0050877 nervous system process — IBA (GO_REF:0000033)

donor token	resolved	own annotations to this term or a descendant
`FB:FBgn0041111`	AFFL_DROME (lilli)	GO:0007611 IMP PMID:18310460; GO:0050877 IBA GO_REF:0000033
`MGI:MGI:1202294`	AFF2_MOUSE (Aff2)	GO:0007611 IMP PMID:11923441; GO:0050877 IBA GO_REF:0000033
`PANTHER:PTN000829417`	panther_tree_node	n/a

GO:0032783 super elongation complex — IBA (GO_REF:0000033)

donor token	resolved	own annotations to this term or a descendant
`FB:FBgn0041111`	AFFL_DROME (lilli)	GO:0032783 IBA GO_REF:0000033; GO:0032783 IPI PMID:22195968; GO:0032783 NAS PMID:28350987
`PANTHER:PTN000829417`	panther_tree_node	n/a

GO:0005634 nucleus — IEA (GO_REF:0000120)

donor token	resolved	own annotations to this term or a descendant
`ARBA:ARBA00026330`	arba_rule	n/a
`InterPro:IPR043640`	interpro_signature	n/a
`UniProtKB-SubCell:SL-0191`	UniProtKB-SubCell	n/a

GO:0005694 chromosome — IEA (GO_REF:0000044)

donor token	resolved	own annotations to this term or a descendant
`UniProtKB-SubCell:SL-0468`	UniProtKB-SubCell	n/a

GO:0010468 regulation of gene expression — IEA (GO_REF:0000002)

donor token	resolved	own annotations to this term or a descendant
`InterPro:IPR007797`	interpro_signature	n/a

GO:0000791 euchromatin — IEA (GO_REF:0000107)

donor token	resolved	own annotations to this term or a descendant
`UniProtKB:Q9ESC8`	AFF4_MOUSE (Aff4)	GO:0000791 IDA PMID:22195968
`ensembl:ENSMUSP00000051479`	ensembl	n/a

GO:0034976 response to endoplasmic reticulum stress — IEA (GO_REF:0000107)

donor token	resolved	own annotations to this term or a descendant
`UniProtKB:A0A8I6GGV9`	A0A8I6GGV9_RAT (Aff4) [TrEMBL]	GO:0034976 IEP PMID:31466050
`ensembl:ENSRNOP00000088228`	ensembl	n/a

GO:0000791 euchromatin — ISS (GO_REF:0000024)

donor token	resolved	own annotations to this term or a descendant
`UniProtKB:Q9ESC8`	AFF4_MOUSE (Aff4)	GO:0000791 IDA PMID:22195968

4. PANTHER node reach

PANTHER:PTN000829417 — 395 annotations over 79 recipient gene products; assignment across terms is UNIFORM.

term	recipients
GO:0003712	79
GO:0006354	79
GO:0006355	79
GO:0032783	79
GO:0050877	79

5. Reference-projection test

For each reference cited by AFF4's GOA (and each donor reference), how many
entities does that reference annotate, and does the functional/phenotype term
spread across the set or stay on the gene actually perturbed? An annotation count
is not an entity count; where the result is too large to page through, the entity
count is reported as unavailable rather than sampled.

PMID:12065898: 2 annotations over 1 entities (subject included: True)
- GO:0005634 EXP [cell] → 1 entities
- GO:0005694 EXP [cell] → 1 entities
PMID:20153263: 12 annotations over 6 entities (subject included: True)
- GO:0005515 IPI [mole] → 6 entities
PMID:21729782: 26 annotations over 17 entities (subject included: True)
- GO:0005515 IPI [mole] → 17 entities
PMID:22190034: 183 annotations over 104 entities (subject included: True)
- GO:0005515 IPI [mole] → 104 entities
PMID:22195968: 61 annotations over 26 entities (subject included: True)
- GO:0008023 IDA [cell] → 16 entities
- GO:0032783 IPI [cell] → 10 entities
- GO:0042795 IMP [biol] → 7 entities
- GO:1905382 NAS [biol] → 5 entities
- GO:0000791 IDA [cell] → 4 entities
- GO:0008023 IPI [cell] → 4 entities
- GO:0005515 IPI [mole] → 3 entities
- GO:0005634 EXP [cell] → 3 entities
- GO:0015030 IDA [cell] → 2 entities
- GO:0003682 IDA [mole] → 2 entities
- GO:0008023 IMP [cell] → 1 entities
- GO:0005694 EXP [cell] → 1 entities
PMID:25416956: 24599 annotations — entity count unavailable; 24599 annotations exceeds the 2000-annotation budget; entity counts unavailable, projection test uninformative here.
PMID:28514442: 3731 annotations — entity count unavailable; 3731 annotations exceeds the 2000-annotation budget; entity counts unavailable, projection test uninformative here.
PMID:33961781: 9514 annotations — entity count unavailable; 9514 annotations exceeds the 2000-annotation budget; entity counts unavailable, projection test uninformative here.
PMID:11171404: 5 annotations over 1 entities (subject included: False)
- GO:0003712 IMP [mole] → 1 entities
- GO:0006355 IMP [biol] → 1 entities
- GO:0007366 IMP [biol] → 1 entities
- GO:0032368 IMP [biol] → 1 entities
- GO:0051493 IMP [biol] → 1 entities
PMID:11923441: 5 annotations over 3 entities (subject included: False)
- GO:0006351 TAS [biol] → 2 entities
- GO:0003700 TAS [mole] → 2 entities
- GO:0007611 IMP [biol] → 1 entities
PMID:18310460: 1 annotations over 1 entities (subject included: False)
- GO:0007611 IMP [biol] → 1 entities
PMID:22547686: 1 annotations over 1 entities (subject included: False)
- GO:0006354 EXP [biol] → 1 entities
PMID:25162227: 6 annotations over 2 entities (subject included: False)
- GO:0003690 IDA [mole] → 1 entities
- GO:0003700 IDA [mole] → 1 entities
- GO:0003700 IMP [mole] → 1 entities
- GO:0006355 IDA [biol] → 1 entities
- GO:0006355 IMP [biol] → 1 entities
- GO:0001764 IDA [biol] → 1 entities
PMID:28350987: 33 annotations over 13 entities (subject included: False)
- GO:0034243 NAS [biol] → 7 entities
- GO:0032783 NAS [cell] → 6 entities
- GO:0097150 IMP [biol] → 5 entities
- GO:0097150 IGI [biol] → 3 entities
- GO:0061629 IPI [mole] → 2 entities
- GO:0007402 IMP [biol] → 2 entities
- GO:0045944 IMP [biol] → 1 entities
- GO:0045944 IGI [biol] → 1 entities
- GO:0003711 NAS [mole] → 1 entities
PMID:31466050: 1 annotations over 1 entities (subject included: False)
- GO:0034976 IEP [biol] → 1 entities
PMID:41062835: 8 annotations over 2 entities (subject included: False)
- GO:0090734 IDA [cell] → 2 entities
- GO:0003711 IMP [mole] → 1 entities
- GO:0006974 IDA [biol] → 1 entities
- GO:0032786 IMP [biol] → 1 entities
- GO:0032968 IMP [biol] → 1 entities
- GO:0000785 IDA [cell] → 1 entities
- GO:0005634 IDA [cell] → 1 entities
PMID:9365243: 2 annotations over 1 entities (subject included: False)
- GO:0045893 IDA [biol] → 1 entities
- GO:0005634 IDA [cell] → 1 entities

5b. GOA uptake of the AFF4 functional literature

For each paper that establishes something about human AFF4: how many GO annotations
does GOA carry from it, over how many entities, and is AFF4 one of them? A row with
AFF4 annotated: False is a paper whose result has not reached AFF4's GO record.

PMID	what it establishes	GOA annotations	entities	AFF4 annotated
PMID:12065898	AFF4/MCEF co-purifies with P-TEFb (CDK9/cyclin T1); nuclear localisation	2	1	True
PMID:20159561	AFF4 is a component of SEC; AFF4 required for SEC stability; knockdown lowers MLL-chimera target genes	1	1	False
PMID:20471948	AFF4 bridges P-TEFb and ELL2 into one bifunctional elongation complex with Tat	0	0	False
PMID:22195968	AFF4 identified in the SEC; SEC vs LEC specialisation for mRNA vs snRNA genes	61	26	True
PMID:22483617	AFF4 binds ELL2 directly and shields it from SIAH1-mediated ubiquitination; AFF4 also binds SIAH1 directly	0	0	False
PMID:23251033	Tat recruits ELL2, ENL/AF9 and P-TEFb via short motifs along the disordered AFF4 axis	0	0	False
PMID:23471103	crystal structure of AFF4 with P-TEFb: AFF4 meanders over cyclin T1, no stable CDK9 contact; interface mutants reduce binding and transcription	0	0	False
PMID:24843025	crystal structure of Tat/P-TEFb/AFF4; AFF4 orders the cyclin T1 TRM and raises Tat-P-TEFb affinity for TAR	0	0	False
PMID:27731797	integrative structure of Tat:AFF4:P-TEFb:TAR; AFF4 helix 2 stabilised without touching the RNA	0	0	False
PMID:28134250	2.0 A crystal structure of the ELL2 C-terminal domain bound to the AFF4 ELLBow	0	0	False
PMID:31147444	2.2 A structure of the AFF4 C-terminal homology domain; mediates AFF4 homo- and AFF1-AFF4 heterodimerisation; CDK9 substrate loop	0	0	False
PMID:32128251	2.4 A structure of AFF4-THD; F1014A/Y1096A abolish dimerisation; dimerisation needed for HIV-1 transactivation	0	0	False
PMID:25730767	CHOPS syndrome: gain-of-function AFF4 missense resistant to SIAH1-mediated degradation; altered genome-wide AFF4/cohesin/RNAP2 binding	0	0	False
PMID:16024815	Aff4-null mice: azoospermia, spermiogenesis arrest, Sertoli-cell expression	2	1	False
PMID:36149892	AFF4 promotes adipogenesis by directly activating ATG5/ATG16L1 transcription; adipose-specific Aff4 knockout	0	0	False
PMID:28955517	AFF4 depletion inhibits and overexpression enhances osteogenic differentiation of human MSCs, with MSC-mediated bone formation in vivo; AFF1 does the opposite	0	0	False
PMID:37528066	AFF1 and AFF4 act antagonistically around the TSS to set elongation rate and termination	0	0	False
PMID:37609817	AFF4 knockdown lowers Ser2-phosphorylated Pol II and increases promoter-proximal pausing genome-wide	0	0	False
PMID:39603240	PNUTS-PP1 dephosphorylates AFF4 Ser-549, promoting Pol II pause release	23	4	False
PMID:22528490	AFF4 induces AMPKalpha2 expression in hypothalamic neurons downstream of ghrelin	0	0	False
PMID:31238957	FUS interacts with AFF4 and forms nuclear condensates with it; FUS restrains AFF4/CDK9 promoter occupancy	0	0	False

Of 21 papers, 16 have produced no GO annotation anywhere in GOA,
and 19 have produced none on AFF4 itself.

PMID	terms it did produce (entities each)
PMID:12065898	GO:0005634 EXP (1); GO:0005694 EXP (1)
PMID:20159561	GO:0032783 IDA (1)
PMID:20471948	nothing
PMID:22195968	GO:0008023 IDA (16); GO:0032783 IPI (10); GO:0042795 IMP (7); GO:1905382 NAS (5); GO:0000791 IDA (4); GO:0008023 IPI (4); GO:0005515 IPI (3); GO:0005634 EXP (3); GO:0015030 IDA (2); GO:0003682 IDA (2); GO:0008023 IMP (1); GO:0005694 EXP (1)
PMID:22483617	nothing
PMID:23251033	nothing
PMID:23471103	nothing
PMID:24843025	nothing
PMID:27731797	nothing
PMID:28134250	nothing
PMID:31147444	nothing
PMID:32128251	nothing
PMID:25730767	nothing
PMID:16024815	GO:0007286 IMP (1); GO:0005634 IDA (1)
PMID:36149892	nothing
PMID:28955517	nothing
PMID:37528066	nothing
PMID:37609817	nothing
PMID:39603240	GO:0001111 IDA (4); GO:0032968 IDA (4); GO:0072357 IDA (4); GO:0004722 IDA (1); GO:0019888 IDA (1); GO:0140767 IDA (1); GO:0000785 IDA (1); GO:0005694 EXP (1)
PMID:22528490	nothing
PMID:31238957	nothing

6. Family coverage: what the AF4/FMR2 members hold experimentally

protein	entry	reviewed	len	annotations	experimental	exp. MF	exp. BP	exp. CC
AFF4 (subject)	AFF4_HUMAN	Swiss-Prot	1163	43	21	6	0	6
AFF1	AFF1_HUMAN	Swiss-Prot	1210	20	13	4	4	5
AFF2	AFF2_HUMAN	Swiss-Prot	1311	18	4	0	3	1
AFF3	AFF3_HUMAN	Swiss-Prot	1226	11	4	0	2	2
mouse Aff4	AFF4_MOUSE	Swiss-Prot	1160	26	6	1	1	4
fly lilli	AFFL_DROME	Swiss-Prot	1673	30	21	2	11	5

AFF4 (subject) experimental rows:
- [MF] GO:0005515 IPI PMID:20153263
- [MF] GO:0005515 IPI PMID:21729782
- [MF] GO:0005515 IPI PMID:22190034
- [MF] GO:0005515 IPI PMID:25416956
- [MF] GO:0005515 IPI PMID:28514442
- [MF] GO:0005515 IPI PMID:33961781
- [CC] GO:0001650 IDA GO_REF:0000052
- [CC] GO:0005634 EXP PMID:12065898
- [CC] GO:0005654 IDA GO_REF:0000052
- [CC] GO:0005694 EXP PMID:12065898
- [CC] GO:0008023 IDA PMID:22195968
- [CC] GO:0016604 IDA GO_REF:0000052

AFF1 experimental rows:
- [MF] GO:0003711 IMP PMID:41062835
- [MF] GO:0005515 IPI PMID:21729782
- [MF] GO:0005515 IPI PMID:22190034
- [MF] GO:0005515 IPI PMID:23260655
- [BP] GO:0006354 EXP PMID:22547686
- [BP] GO:0006974 IDA PMID:41062835
- [BP] GO:0032786 IMP PMID:41062835
- [BP] GO:0032968 IMP PMID:41062835
- [CC] GO:0000785 IDA PMID:41062835
- [CC] GO:0005634 IDA PMID:41062835
- [CC] GO:0008023 IDA PMID:22195968
- [CC] GO:0032783 IDA PMID:20159561
- [CC] GO:0090734 IDA PMID:41062835

AFF2 experimental rows:
- [BP] GO:0010468 IMP PMID:23562910
- [BP] GO:0035063 IMP PMID:23562910
- [BP] GO:0043484 IMP PMID:19136466
- [CC] GO:0016607 IDA PMID:19136466

AFF3 experimental rows:
- [BP] GO:0034612 IMP PMID:20444755
- [BP] GO:0035116 IMP PMID:18616733
- [CC] GO:0005634 IDA PMID:8555498
- [CC] GO:0005654 IDA GO_REF:0000052

mouse Aff4 experimental rows:
- [MF] GO:0005515 IPI PMID:23273992
- [BP] GO:0007286 IMP PMID:16024815
- [CC] GO:0000791 IDA PMID:22195968
- [CC] GO:0005634 EXP PMID:22195968
- [CC] GO:0005634 IDA PMID:16024815
- [CC] GO:0005694 EXP PMID:22195968

fly lilli experimental rows:
- [MF] GO:0003712 IMP PMID:11171404
- [MF] GO:0061629 IPI PMID:28350987
- [BP] GO:0006355 IMP PMID:11171404
- [BP] GO:0007366 IMP PMID:11171404
- [BP] GO:0007379 HMP PMID:15166158
- [BP] GO:0007611 IMP PMID:18310460
- [BP] GO:0032368 IMP PMID:11171404
- [BP] GO:0045944 IGI PMID:28350987
- [BP] GO:0045944 IMP PMID:28350987
- [BP] GO:0048190 IGI PMID:18202376
- [BP] GO:0051493 IMP PMID:11171404
- [BP] GO:0097150 IGI PMID:28350987
- [BP] GO:0097150 IMP PMID:28350987
- [CC] GO:0000791 IDA PMID:22195968
- [CC] GO:0000791 IDA PMID:23932780
- [CC] GO:0005634 IDA PMID:11171403
- [CC] GO:0008023 IDA PMID:22195968
- [CC] GO:0032783 IPI PMID:22195968

7. `GO:0005515` partners: expanded IntAct records

AFF4 has 207 IntAct interaction records spanning
86 distinct partner molecules. GOA exports
9 of them as GO:0005515 IPI rows.

NbExp is not used here: it has been observed to count sub-methods of a single
screen, replicates, and even domains of one protein. Distinct publications and
distinct (publication, method) pairs are counted instead.

partner	records	distinct pubs	(pub/method) pairs	MI score(s)	promiscuity (IntAct records for the partner)
CCNT1 (O60563)	8	4	6	0.81	263
tat (P04608)	4	1	2	0.56	95
MLLT3 (P42568)	4	2	2	0.56	181
AP2B1 (P63010)	3	1	3	0.56	537
MLLT1 (Q03111)	11	3	5	0.76	148
GOLGA2 (Q08379)	3	1	3	0.56	2335
TRAF2 (Q12933)	3	1	3	0.56	1727
MTUS2 (Q5JR59)	3	1	3	0.56	1476
SIAH1 (Q8IUQ4)	5	1	3	0.56	474

CCNT1 (O60563): pubs ['20153263', '21729782', '28514442', '33961781']; methods ['affinity chrom', 'anti bait coip', 'anti tag coip']; pub/method pairs ['20153263/affinity chrom', '20153263/anti bait coip', '20153263/anti tag coip', '21729782/anti tag coip', '28514442/anti tag coip', '33961781/anti tag coip']
tat (P04608): pubs ['22190034']; methods ['anti tag coip', 'pull down']; pub/method pairs ['22190034/anti tag coip', '22190034/pull down']
MLLT3 (P42568): pubs ['20153263', '21729782']; methods ['anti tag coip']; pub/method pairs ['20153263/anti tag coip', '21729782/anti tag coip']
AP2B1 (P63010): pubs ['25416956']; methods ['two hybrid array', 'two hybrid prey pooling approach', 'validated two hybrid']; pub/method pairs ['25416956/two hybrid array', '25416956/two hybrid prey pooling approach', '25416956/validated two hybrid']
MLLT1 (Q03111): pubs ['20153263', '21729782', '33961781']; methods ['affinity chrom', 'anti bait coip', 'anti tag coip']; pub/method pairs ['20153263/affinity chrom', '20153263/anti bait coip', '20153263/anti tag coip', '21729782/anti tag coip', '33961781/anti tag coip']
GOLGA2 (Q08379): pubs ['25416956']; methods ['two hybrid array', 'two hybrid prey pooling approach', 'validated two hybrid']; pub/method pairs ['25416956/two hybrid array', '25416956/two hybrid prey pooling approach', '25416956/validated two hybrid']
TRAF2 (Q12933): pubs ['25416956']; methods ['two hybrid array', 'two hybrid prey pooling approach', 'validated two hybrid']; pub/method pairs ['25416956/two hybrid array', '25416956/two hybrid prey pooling approach', '25416956/validated two hybrid']
MTUS2 (Q5JR59): pubs ['25416956']; methods ['two hybrid array', 'two hybrid prey pooling approach', 'validated two hybrid']; pub/method pairs ['25416956/two hybrid array', '25416956/two hybrid prey pooling approach', '25416956/validated two hybrid']
SIAH1 (Q8IUQ4): pubs ['25416956']; methods ['two hybrid array', 'two hybrid prey pooling approach', 'validated two hybrid']; pub/method pairs ['25416956/two hybrid array', '25416956/two hybrid prey pooling approach', '25416956/validated two hybrid']

IntAct partners of AFF4 that carry no GO:0005515 row in AFF4's GOA (spoke-expanded co-IP records are not exported as IPI):

A0JLT2:MED19
A3KMF4:Aff1
A5YKK6:CNOT1
CHEBI:39112:bosutinib
CHEBI:45783:imatinib
EBI-2890930:mll_af9_human_protein
ENSG00000113739:stc2_human_gene
ENSG00000136997:myc_human_gene
ENSG00000186352:anr37_human_gene
ENSG00000235941:hsp70_human_gene
O00472:ELL2
O00541:PES1
O00560:SDCBP
O60583-2:CCNT2
O60583:CCNT2
O94992:HEXIM1
O95218:ZRANB2
O95402:MED26
P03372:ESR1
P07910:HNRNPC
P0C0S5:H2AZ1
P0DMU7:CT45A6
P10275:AR
P16401:H1-5
P21741:MDK
P28702:RXRB
P32121-3:ARRB2
P32121:ARRB2
P35226:BMI1
P40425:PBX2
P43250:GRK6
P48426:PIP4K2A
P50750-2:CDK9
P50750:CDK9
P51825:AFF1
P55199:ELL
P61328:FGF12
P68431:H3C1
Q03164-PRO_0000390949:Q03164-PRO_0000390949
Q06187:BTK
Q06787:FMR1
Q14201:BTG3
Q15283:RASA2
Q2KHN1:RNF151
Q5S007:LRRK2
Q5VWQ0:RSBN1
Q6PD62:CTR9
Q86VH4:LRRTM4
Q8IY18:SMC5
Q8IZU1:FAM9A
Q8N3E9:PLCD3
Q8N9B5:JMY
Q8N9E0:FAM133A
Q8N9I0:SYT2
Q8NCB2-2:CAMKV
Q8NCB2:CAMKV
Q8TBX8:PIP4K2C
Q8WUA2:PPIL4
Q92838:EDA
Q92917:GPKOW
Q93079:H2BC9
Q96CJ1:EAF2
Q96JC9:EAF1
Q96Q40:CDK15
Q9BRC7:PLCD4
Q9BTT4:MED10
Q9BYN8:MRPS26
Q9ERL0:Mllt1
Q9H4F8:SMOC1
Q9H4G0:EPB41L1
Q9H6A0:DENND2D
Q9HB65:ELL3
Q9HCM4-2:EPB41L5
Q9NX58:LYAR
Q9UBC1:NFKBIL1
Q9UER7:DAXX
Q9Y2J2:EPB41L3

7b. Is spoke expansion the whole export rule? Tested in both directions

every GOA GO:0005515 partner has a non-spoke-expanded record: True
spoke expansion is the WHOLE export rule: False
ELL2 is an IntAct partner: True; has a non-spoke-expanded record: False
partners with a non-spoke-expanded record yet absent from GOA: ['O00560', 'P0C0S5', 'P16401', 'Q06787', 'Q14201', 'Q5S007', 'Q93079']

Spoke-expansion-only is SUFFICIENT to explain a specific absence such as ELL2's, because every GOA GO:0005515 partner has at least one non-spoke-expanded record while ELL2 has none. It is NOT the whole export rule: other partners do have non-spoke-expanded records and are still absent from GOA, so a further filter operates that this analysis does not identify.

8. Retraction / erratum / expression-of-concern check

PMIDs checked: 32
positive controls that fired: ['17994018', '32125225', '36563143'] (a retraction, an erratum with a PMID, and a corrigendum with a NULL PMID)
PMIDs with any flag: 2
- 28955517: {'pubtype_flags': [], 'comments_corrections': [{'ref_type': 'ErratumIn', 'pmid': '32257529'}]}
- 32257529: {'pubtype_flags': ['Published Erratum'], 'comments_corrections': [{'ref_type': 'ErratumFor', 'pmid': '28955517'}]}

2 cited reference(s) carry a correction and must be flagged in the review. The three controls fired in the same call pattern, so the detector is working in both directions rather than only reporting nulls.

9. Ontology relations the review depends on

Fetched and asserted, never inferred from a label.

claim	child	parent	parent is ancestor?	expected
Pol II elongation is_a DNA-templated elongation	GO:0006368	GO:0006354	True	True
positive reg. of Pol II elongation under reg. of transcription	GO:0032968	GO:0006355	True	True
SEC is_a transcription elongation factor complex	GO:0032783	GO:0008023	True	True
reg. of transcription under reg. of gene expression	GO:0006355	GO:0010468	True	True
learning or memory under nervous system process	GO:0007611	GO:0050877	True	True
elongation factor activity is NOT under coregulator activity	GO:0003711	GO:0003712	False	False
...and not the other way either: they are SIBLINGS	GO:0003712	GO:0003711	False	False
adaptor activity is NOT under protein binding	GO:0030674	GO:0005515	False	False

10. Is `GO:0030332 cyclin binding` usable for cyclin T1?

The term's definition specifies cyclins "whose levels in a cell varies markedly
during the cell cycle, rising steadily until mitosis, then falling abruptly to
zero" — which does not describe the transcriptional cyclin T1. Usage agrees:

protein	GO:0030332 annotations (incl. descendants)	evidence
CDK9 (P50750)	0	-
HEXIM1 (O94992)	0	-
BRD4 (O60885)	0	-
CDK2 (positive control: cell-cycle CDK) (P24941)	5	IDA, IEA, IPI

The cell-cycle CDK is the positive control, so the zeros for the cyclin T1 binders
are a measurement rather than a failed query.

11. `GO:0043923 host-mediated activation of viral transcription`

human annotations: 20
human entities: 18 (17 proteins + complexes ['ComplexPortal:CPX-222'])
AFF4 holds it: False

An annotation count is not an entity count; both are reported so the table below cannot be read as a count of proteins.

symbol	evidence	reference	assigned by
CCNT1	IDA	PMID:10866664	ComplexPortal
CCNT1	NAS	PMID:25116364	ParkinsonsUK-UCL
CDK9	IDA	PMID:10866664	ComplexPortal
CHD1	IMP	PMID:25297984	CACAO
CTDP1	IDA	PMID:15723517	CAFA
EP300	IDA	PMID:16687403	BHF-UCL
HPN	IDA	PMID:15614436	UniProt
JUN	IDA	PMID:2833704	UniProt
LEF1	IDA	PMID:7657162	UniProt
NUCKS1	IGI	PMID:25116364	ParkinsonsUK-UCL
RRP1B	IMP	PMID:26311876	UniProt
SMARCA4	IMP	PMID:16687403	BHF-UCL
SMARCB1	IMP	PMID:16687403	BHF-UCL
SNW1	IDA	PMID:15905409	UniProt
SNW1	IMP	PMID:19818711	UniProt
SP1	IDA	PMID:2833704	UniProt
TAF11	IDA	PMID:9108034	UniProt
TFAP4	IDA	PMID:2833704	UniProt
ZNF639	IMP	PMID:20484494	UniProt
ccnt1-cdk9_human	IDA	PMID:10866664	ComplexPortal

11b. Which InterPro signature supplies which term (interpro2go)

Signatures read off AFF4's own DR InterPro; lines. The entries that map to
nothing are the control showing the pipeline is capable of restraint.

mapping lines in the downloaded interpro2go: 30122
any signature mapped to a molecular function: False

signature	maps to
IPR007797	GO:0010468 regulation of gene expression [biol]
IPR043639	nothing
IPR043640	GO:0005634 nucleus [cell]

12. `file:` quote check against `AFF4-uniprot.txt`

The repo's reference validator checks supporting_text verbatim only for PMID:
references; file: quotes are skipped entirely, which makes them the one place in
the document where an invented or line-wrapped quotation survives every automated
gate. Each quote below is asserted present on ONE physical line, and the check
raises if it is ever handed an empty quote list.

quote	line(s)
`SUBCELLULAR LOCATION: Nucleus {ECO:0000269\|PubMed:12065898}.`	[349]
`SIMILARITY: Belongs to the AF4 family. {ECO:0000305}.`	[377]
`DR PDB; 5JW9; X-ray; 2.00 A; A=301-351.`	[404]
`DR PDB; 6KN5; X-ray; 2.20 A; A=899-1163.`	[408]
`DR PDB; 6R80; X-ray; 2.20 A; A=899-1163.`	[409]
`DR PDB; 4IMY; X-ray; 2.94 A; G/H/I=2-73.`	[401]
`DR PDB; 4OGR; X-ray; 3.00 A; C/G/L=2-73.`	[402]
`PE 1: Evidence at protein level;`	[511]