AEBP2 (Q6ZN18) — provenance analysis of the GO annotation set

Generated by analyze_aebp2.py. Every number below is computed at run time;
nothing is hardcoded from a previous run. The tables are the claims — the
surrounding prose only names what was measured.

1. Row reconciliation (run first, before any reviewing)

quantity value
GOA TSV data rows 20
GOA TSV distinct rows 20
QuickGO annotation count for Q6ZN18 20
existing_annotations entries in the review YAML 22
of which are this review's own NEW proposals 2
entries covering existing GOA rows 20

Evidence census: {'IEA': 3, 'NAS': 6, 'IBA': 2, 'ISA': 1, 'EXP': 1, 'IDA': 2, 'TAS': 3, 'IPI': 2}

Aspect census: {'cellular_component': 14, 'biological_process': 6}

No GO:0005515 protein binding row exists, so the stub's known
WITH/FROM-blind collapse of partner rows cannot have occurred here, and the
three counts reconcile exactly.

2. WITH/FROM resolution (built from the TSV field, not by hand)

9 distinct tokens; unresolved: none

token kind resolves to reviewed length organism
ARBA:ARBA00089504 arba_rule ['GO:0035098'] — — —
FB:FBgn0086655 MOD gene id (5 candidates, 4 unreviewed also returned) JING_DROME (jing) True 1486 Drosophila melanogaster
MGI:MGI:1338038 MOD gene id (4 candidates, 3 unreviewed also returned) AEBP2_MOUSE (Aebp2) True 504 Mus musculus
PANTHER:PTN002323211 panther_tree_node an internal PANTHER tree node, not a protein — — —
UniProtKB-SubCell:SL-0191 controlled_vocabulary_id a vocabulary term, not a gene product — — —
UniProtKB:Q6ZN18 UniProt accession (self-reference) AEBP2_HUMAN (AEBP2) True 517 Homo sapiens
UniProtKB:Q9Z248 UniProt accession AEBP2_MOUSE (Aebp2) True 504 Mus musculus
ensembl:ENSMUSP00000084896 MOD gene id (1 candidates, 0 unreviewed also returned) AEBP2_MOUSE (Aebp2) True 504 Mus musculus
tfclass:2.3.2 controlled_vocabulary_id a vocabulary term, not a gene product — — —

3. IBA donor evidence — which term does each donor actually hold?

donor term asked rows its own experimental rows
mouse Aebp2 GO:0035098 6 IDA GO:0035098 PMID:20064375; IDA GO:0035098 PMID:20064376; IDA GO:0035098 PMID:31451685
mouse Aebp2 GO:0006357 2 IMP GO:0000122 PMID:10329662
mouse Aebp2 GO:0000122 1 IMP GO:0000122 PMID:10329662
Drosophila jing GO:0006357 4 IMP GO:0000122 PMID:16510782; IMP GO:0045944 PMID:21061018
Drosophila jing GO:0035098 2 none

Positive control: EZH2 Q15910 x GO:0035098(descendants) returns 9 rows, so a zero above would be a real zero.

Donor directions for GO:0006357: ['negative', 'positive']. LCA-of-disagreeing-donors: True.

4. PANTHER node reach — what the node gave, and to whom

PANTHER:PTN002323211: 196 annotations over 117 recipients.

recipient group n
receives both GO:0006357 and GO:0035098 79
receives GO:0006357 only 38
other term sets 0

Subject receives: ['GO:0006357', 'GO:0035098'].

5. Reference-projection test (fully paginated)

A reference that annotates the complex plus every subunit with an
identical term set is a projection, not N independent findings. The second
question matters as much as the first: does the functional term spread
across the set, or stay on the entity that was actually perturbed?

reference annotations entities ComplexPortal complex entities assigned by dominant term-set signature
PMID:33514705 38 9 2 {'ComplexPortal': 35, 'DisProt': 3} 4 terms × 5 entities
PMID:29348366 35 9 2 {'ComplexPortal': 35} 4 terms × 6 entities
PMID:20075857 23 12 0 {'IntAct': 12, 'UniProt': 11} 1 terms × 5 entities
PMID:29499137 4 4 0 {'UniProt': 4} 1 terms × 4 entities
PMID:10329662 5 1 0 {'MGI': 4, 'NTNU_SB': 1} 4 terms × 1 entities
GO_REF:0000113 1436 727 0 {'NTNU_SB': 1436} 2 terms × 709 entities

6. TFClass / DbTF census — testing the zinc-finger over-annotation lead

GO_REF:0000113 (TFClass-based DbTF curation, NTNU_SB) covers
727 human gene products in 1436 annotations.

group n %
receives GO:0000981 DNA-binding transcription factor activity 709 97.5%
receives GO:0000785 chromatin only 18 2.5%

AEBP2 is in the withheld set (subject_in_withheld_set = True), receiving ['GO:0000785']. The withheld set:

accession gene name
O15105 SMAD7 SMAD family member 7
O43541 SMAD6 SMAD family member 6
P51843 NR0B1 Nuclear receptor subfamily 0 group B member 1
P61129 ZC3H6 Zinc finger CCCH domain-containing protein 6
Q12986 NFX1 Transcriptional repressor NF-X1
Q15466 NR0B2 Nuclear receptor subfamily 0 group B member 2
Q15596 NCOA2 Nuclear receptor coactivator 2
Q15788 NCOA1 Nuclear receptor coactivator 1
Q5H9I0 TFDP3 Transcription factor Dp family member 3
Q5HYR2 DMRTC1 Doublesex- and mab-3-related transcription factor C1
Q6NT76 HMBOX1 Homeobox-containing protein 1
Q6ZN18 AEBP2 Zinc finger protein AEBP2
Q6ZNB6 NFXL1 NF-X1-type zinc finger protein NFXL1
Q8IX07 ZFPM1 Zinc finger protein ZFPM1
Q8N5P1 ZC3H8 Zinc finger CCCH domain-containing protein 8
Q8WW38 ZFPM2 Zinc finger protein ZFPM2
Q9BPY8 HOPX Homeodomain-only protein
Q9Y6Q9 NCOA3 Nuclear receptor coactivator 3

7. Molecular-function census across PRC2

subunit accession total rows MF rows MF terms
EZH2 Q15910 169 94 15 distinct
RBBP4 Q09028 196 63 6 distinct
EED O75530 91 47 6 distinct
EZH1 Q92800 72 43 11 distinct
SUZ12 Q15022 87 39 5 distinct
PHF19 Q5T6S3 55 36 5 distinct
RBBP7 Q16576 135 31 2 distinct
PALI1(LCOR) Q86SE9 45 25 2 distinct
EPOP Q8N7C0 17 9 4 distinct
JARID2 Q92833 35 7 4 distinct
MTF2 Q9Y483 28 5 5 distinct
AEBP2 Q6ZN18 20 0 0 distinct

Subunits with zero molecular-function rows: ['AEBP2'].

GO:0031507 held by NAS alone: ['AEBP2', 'JARID2', 'MTF2', 'PALI1(LCOR)', 'PHF19', 'RBBP4', 'RBBP7', 'SUZ12']. Held with other evidence: ['EED', 'EZH1', 'EZH2'].

8. GO:0180000 — the proposed term and its precedent

GO:0180000 histone methyltransferase inhibitor activity — obsolete: False; secondaryIds: None

Binds to and stops, prevents or reduces the activity of a histone methyltransferase.

Holders in GOA: 15 annotations over symbols ['A0A0D9RJU4', 'A0A2K5DD87', 'A0A2K6TH71', 'A0A2R8ZCM4', 'A0A8I5NQA2', 'EZHIP', 'Ezhip', 'F7ICH9', 'G3QYW7']. Experimental anchors:

entity symbol evidence reference
UniProtKB:Q86X51 EZHIP IDA PMID:30923826

Subject already holds it: False.

9. Logical-opposite citation cross-product

pair both present shared references full cross-product
GO:0000122 / GO:0045944 False none False
GO:0045892 / GO:0045893 False none False
GO:0031507 / GO:0031508 False none False

Result: no logically opposed pair is co-annotated on this gene. This is a reported negative: the check ran and
found nothing, which is a different fact from the check having been skipped.
The detector demonstrably sees a synthetic cross-product (True), so the negative
is not the silence of a broken comparison.

10. PDB construct census — which AEBP2 was in each structure

17 PDB entries resolve an AEBP2 chain mapped to Q6ZN18.

PDB released primary citation AEBP2 range(s) vs Q6ZN18
6C23 2018-01-24 PMID:29348366 209–503
6C24 2018-01-24 PMID:29348366 209–503
5WAI 2018-03-14 PMID:29499137 407–503
5Y1U 2018-04-18 PMID:29134516 379–390
5Y0U 2018-08-01 PMID:29134516 258–357
6WKR 2021-02-03 PMID:33479123 209–503
7KSO 2021-02-03 PMID:33514705 209–503
8FYH 2023-10-04 PMID:37733873 1–517
8EQV 2024-07-31 PMID:41168462 1–517
9C8U 2024-09-04 PMID:39231985 210–503
8T9G 2024-09-25 PMID:39303719 223–517
8TAS 2024-09-25 PMID:39303719 224–517
8TB9 2024-09-25 PMID:39303719 223–517
8VMI 2025-01-15 PMID:39774834 223–517
8VNZ 2025-01-15 PMID:39774834 223–517
8VNV 2025-01-22 PMID:39774834 225–503
9DCH 2025-03-12 PMID:39257770 210–503

Full length from residue 1: 2. N-terminally truncated: 15 (construct starts at [209, 210, 223, 224, 225, 258, 379, 407]).

Full-length entries whose primary citation is PMID:41168462 (the AEBP2L paper): ['8EQV'].

11. Isoform mapping

Canonical length 517 aa; 3 C2H2 zinc fingers at [(261, 286), (300, 322), (328, 352)].

isoform UniProt id VAR_SEQ
1 Q6ZN18-1 displayed
2 Q6ZN18-2 VSP_034359
3 Q6ZN18-3 VSP_034357, VSP_034358

Isoform 2's deletion [504, 517] overlaps the [495, 517] region UniProt annotates as important for nucleosome binding activity of the PRC2 complex by 14 of 23 residues.

Isoform 3 deletes [1, 216], leaving 301 residues.

12. Which ARBA condition set fires

ARBA00089504 asserts exactly ['GO:0035098'] and has 8 alternative condition sets, each a FunFam-id + taxon conjunction with no residue, interaction or assay term in it.

The subject's own FunFam cross-references: ['3.30.160.60:FF:000323', '3.30.160.60:FF:000471'].

condition set FunFams required taxon conditions
[3] (fires on Q6ZN18) ['3.30.160.60:FF:000323', '3.30.160.60:FF:000471'] ['Eukaryota', 'NOT Ascomycota']

All condition sets, for context: