Global IEP atlas

Global IEP atlas

Generated by iep_global_atlas.py. The complete set of 25,401 annotations that a GAF labels IEP, downloaded from QuickGO with evidenceCode=ECO:0000270&evidenceCodeUsage=descendants and then filtered to GO EVIDENCE CODE == IEP. This is the denominator for the review-driven sample measured in iep-corpus-survey.md.

GOA snapshot: 2026-07-27 (data/global_iep_annotations.tsv, committed so the figures below stay reproducible as GOA moves; delete it to re-download). GO closure computed against GO release 2026-07-26.

One set of figures is not frozen by that snapshot: the IEP-dependence shares divide the snapshot's IEP count for a term by a live QuickGO count of all annotations to that term, so they drift as GOA grows.

Scale

Global (UniProt-GOA) Repo (genes/*/*/*-goa.tsv) Coverage
IEP annotations 25,401 555 2.2%
Gene products with IEP 10,618 218 2.1%
Gene directories with IEP — 220 —
Distinct GO terms 2,383 288 12.1%
Distinct references 11,777 368 3.1%

Not all of it is in scope for a protein-centric review corpus:

Gene product database IEP rows Share Distinct products
UniProtKB 24,561 96.7% 10,181
RNAcentral 840 3.3% 437

What GAFs call IEP is not one ECO class

Of the 25,401 annotations a GAF labels IEP, 23,747 (93.5%) are literally ECO:0000270; the remaining 1,654 (6.5%) use a more specific descendant class that collapses to IEP in the GAF projection. The aspect breakdown shows why this matters.

ECO class IEP rows biological_process molecular_function cellular_component
ECO:0000270 23,747 23,691 36 20
ECO:0000279 1,417 285 22 1,110
ECO:0005657 52 52 0 0
ECO:0005653 47 46 1 0
ECO:0005648 35 30 5 0
ECO:0005636 32 32 0 0
ECO:0001838 23 19 0 4
ECO:0005633 18 0 12 6
ECO:0005641 11 11 0 0
ECO:0001182 7 4 0 3
ECO:0005617 3 3 0 0
ECO:0000282 2 2 0 0

Sampling bias of the reviewed corpus

Repo / global is the ratio of shares: 1.00x means the repo samples that stratum in proportion to its global frequency, >1 over-samples it, <1 under-samples it.

By assigning group

Stratum Global rows Global % Repo rows Repo % Repo / global
RGD 11,198 44.1% 178 32.1% 0.73x
UniProt 4,525 17.8% 160 28.8% 1.62x
TAIR 3,071 12.1% 95 17.1% 1.42x
SynGO 1,388 5.5% 22 4.0% 0.73x
FlyBase 1,050 4.1% 7 1.3% 0.31x
MGI 876 3.4% 14 2.5% 0.73x
AgBase 785 3.1% 0 0.0% 0.00x
EcoCyc 419 1.6% 2 0.4% 0.22x
ZFIN 326 1.3% 0 0.0% 0.00x
BHF-UCL 258 1.0% 15 2.7% 2.66x
CollecTF 211 0.8% 0 0.0% 0.00x
EcoliWiki 191 0.8% 4 0.7% 0.96x

Absent from the repo entirely: AgBase, ZFIN, CollecTF.

By taxon

Stratum Global rows Global % Repo rows Repo % Repo / global
Rattus norvegicus 12,054 47.5% 190 34.2% 0.72x
Arabidopsis thaliana 5,016 19.7% 154 27.7% 1.41x
Mus musculus 2,043 8.0% 27 4.9% 0.60x
Drosophila melanogaster 1,120 4.4% 7 1.3% 0.29x
Homo sapiens 932 3.7% 101 18.2% 4.96x
Escherichia coli K-12 621 2.4% 6 1.1% 0.44x
Gossypium hirsutum 395 1.6% 0 0.0% 0.00x
Danio rerio 335 1.3% 0 0.0% 0.00x
Oryza sativa Japonica Group 334 1.3% 4 0.7% 0.55x
Gallus gallus 279 1.1% 0 0.0% 0.00x
Mycobacterium tuberculosis H37Rv 179 0.7% 0 0.0% 0.00x
Dictyostelium discoideum 174 0.7% 23 4.1% 6.05x

Absent from the repo entirely: Gossypium hirsutum, Danio rerio, Gallus gallus, Mycobacterium tuberculosis H37Rv.

By GO aspect

Stratum Global rows Global % Repo rows Repo % Repo / global
biological_process 24,178 95.2% 532 95.9% 1.01x
cellular_component 1,147 4.5% 20 3.6% 0.80x
molecular_function 76 0.3% 3 0.5% 1.81x

By qualifier

Stratum Global rows Global % Repo rows Repo % Repo / global
involved_in 19,124 75.3% 400 72.1% 0.96x
acts_upstream_of_or_within 4,842 19.1% 128 23.1% 1.21x
is_active_in 1,122 4.4% 20 3.6% 0.82x
NOT involved_in 169 0.7% 2 0.4%
enables 76 0.3% 3 0.5% 1.81x
acts_upstream_of_negative_effect 19 0.1% 2 0.4% 4.82x
located_in 19 0.1% 0 0.0% 0.00x
acts_upstream_of_positive_effect 16 0.1% 0 0.0% 0.00x

Absent from the repo entirely: located_in, acts_upstream_of_positive_effect.

By GO branch

Stratum Global rows Global % Repo rows Repo % Repo / global
response to stimulus 17,099 67.3% 379 68.3% 1.01x
developmental process 4,110 16.2% 84 15.1% 0.94x
unclassified 1,395 5.5% 24 4.3% 0.79x
cellular component 1,147 4.5% 20 3.6% 0.80x
biological regulation 1,041 4.1% 33 5.9% 1.45x
metabolic process 403 1.6% 6 1.1% 0.68x
localization 130 0.5% 6 1.1% 2.11x
molecular function 76 0.3% 3 0.5% 1.81x

By GO term (global top 30)

GO term Label Global Global % Repo Repo / global
GO:0009410 response to xenobiotic stimulus 512 2.02% 10 0.89x
GO:0009409 response to cold 387 1.52% 7 0.83x
GO:0009617 response to bacterium 384 1.51% 10 1.19x
GO:0009737 response to abscisic acid 379 1.49% 6 0.72x
GO:0098978 glutamatergic synapse 358 1.41% 5 0.64x
GO:0045471 response to ethanol 347 1.37% 5 0.66x
GO:0009611 response to wounding 343 1.35% 8 1.07x
GO:0001666 response to hypoxia 310 1.22% 4 0.59x
GO:1990830 cellular response to leukemia inhibitory factor 294 1.16% 3 0.47x
GO:0009414 response to water deprivation 283 1.11% 2 0.32x
GO:0009651 response to salt stress 267 1.05% 3 0.51x
GO:0009408 response to heat 259 1.02% 25 4.42x
GO:0007623 circadian rhythm 257 1.01% 5 0.89x
GO:0009753 response to jasmonic acid 252 0.99% 6 1.09x
GO:0032355 response to estradiol 225 0.89% 3 0.61x
GO:0006974 DNA damage response 217 0.85% 2 0.42x
GO:0032496 response to lipopolysaccharide 204 0.80% 2 0.45x
GO:0071456 cellular response to hypoxia 199 0.78% 3 0.69x
GO:0031667 response to nutrient levels 192 0.76% 1 0.24x
GO:0007283 spermatogenesis 167 0.66% 1 0.27x
GO:0009416 response to light stimulus 166 0.65% 3 0.83x
GO:0009751 response to salicylic acid 163 0.64% 5 1.40x
GO:0009733 response to auxin 162 0.64% 6 1.70x
GO:0006979 response to oxidative stress 145 0.57% 4 1.26x
GO:0060291 long-term synaptic potentiation 139 0.55% 5 1.65x
GO:0007584 response to nutrient 137 0.54% 1 0.33x
GO:0090378 seed trichome elongation 135 0.53% 0 0.00x
GO:0045892 negative regulation of DNA-templated transcription 132 0.52% 0 0.00x
GO:0009636 response to toxic substance 132 0.52% 0 0.00x
GO:0042542 response to hydrogen peroxide 130 0.51% 5 1.76x

How dependent is each term on IEP?

For each of the most frequent IEP terms, the share of all direct UniProt-GOA annotations to that term that are IEP. A high share means IEP is the term's main support rather than corroboration for it.

GO term Label IEP All evidence IEP share
GO:0090378 seed trichome elongation 135 689 19.6%
GO:0045471 response to ethanol 347 2,237 15.5%
GO:1990830 cellular response to leukemia inhibitory factor 294 2,152 13.7%
GO:0009620 response to fungus 113 1,419 8.0%
GO:0051384 response to glucocorticoid 109 1,541 7.1%
GO:0043434 response to peptide hormone 117 1,703 6.9%
GO:0009753 response to jasmonic acid 252 4,152 6.1%
GO:0009612 response to mechanical stimulus 128 2,791 4.6%
GO:0007565 female pregnancy 120 2,715 4.4%
GO:0032355 response to estradiol 225 6,394 3.5%
GO:0032496 response to lipopolysaccharide 204 6,096 3.3%
GO:0009410 response to xenobiotic stimulus 512 15,787 3.2%
GO:0009751 response to salicylic acid 163 6,263 2.6%
GO:0031667 response to nutrient levels 192 7,852 2.4%
GO:0071260 cellular response to mechanical stimulus 121 6,547 1.8%
GO:0009737 response to abscisic acid 379 20,647 1.8%
GO:0060291 long-term synaptic potentiation 139 7,727 1.8%
GO:0009617 response to bacterium 384 23,974 1.6%
GO:0009611 response to wounding 343 21,845 1.6%
GO:0009414 response to water deprivation 283 22,125 1.3%
GO:0009651 response to salt stress 267 21,875 1.2%
GO:0071356 cellular response to tumor necrosis factor 121 11,183 1.1%
GO:0007584 response to nutrient 137 12,930 1.1%
GO:0071456 cellular response to hypoxia 199 19,367 1.0%
GO:0046686 response to cadmium ion 129 12,744 1.0%
GO:0001666 response to hypoxia 310 32,023 1.0%
GO:0009723 response to ethylene 110 11,645 0.9%
GO:0009409 response to cold 387 42,638 0.9%
GO:0007623 circadian rhythm 257 32,786 0.8%
GO:0009636 response to toxic substance 132 18,364 0.7%
GO:0009416 response to light stimulus 166 29,812 0.6%
GO:0071222 cellular response to lipopolysaccharide 129 29,469 0.4%
GO:0007283 spermatogenesis 167 41,992 0.4%
GO:0098978 glutamatergic synapse 358 92,943 0.4%
GO:0042542 response to hydrogen peroxide 130 37,066 0.4%
GO:0009733 response to auxin 162 47,644 0.3%
GO:0009408 response to heat 259 110,529 0.2%
GO:0006974 DNA damage response 217 385,029 0.1%
GO:0006979 response to oxidative stress 145 326,427 0.0%
GO:0045892 negative regulation of DNA-templated transcription 132 738,511 0.0%

Concentration

Highest-yield references

Reference IEP rows Gene products Distinct terms
PMID:20439489 291 291 1
PMID:23012479 153 153 1
PMID:11967071 152 152 1
PMID:25858512 130 130 1
PMID:23646144 100 100 1
PMID:11486054 72 72 1
PMID:24205035 69 59 2
PMID:31001913 61 11 7
PMID:19545574 52 26 2
PMID:26442059 50 17 6
PMID:26687361 47 47 1
PMID:18507812 41 7 8
PMID:21029107 40 4 10
PMID:19682768 39 3 14
PMID:22634043 38 38 1

Gene products with the largest IEP load

Gene product Symbol Taxon IEP rows In repo
Q9QYK2 Ppargc1a Rattus norvegicus 50 no
P20607 Il6 Rattus norvegicus 48 no
Q62600 Nos3 Rattus norvegicus 45 no
P20961 Serpine1 Rattus norvegicus 44 no
P16599 Tnf Rattus norvegicus 43 no
P97826 Star Rattus norvegicus 43 no
O35800 Hif1a Rattus norvegicus 41 no
P14844 Ccl2 Rattus norvegicus 40 no
P14137 Cyp11a1 Rattus norvegicus 39 no
P22071 Hsd3b1 Rattus norvegicus 39 no
Q63264 Il1b Rattus norvegicus 39 no
A0A8I6ATW0 Abcb4 Rattus norvegicus 38 no
A0A9K3Y745 Abcb1a Rattus norvegicus 38 no
A0ABK0KW61 Abcb1a Rattus norvegicus 38 no
A0ABK0KWF9 Abcb4 Rattus norvegicus 38 no
A0ABK0M473 Bcl2 Rattus norvegicus 38 no
G3V9C8 Abcb4 Rattus norvegicus 38 no
P04177 Th Rattus norvegicus 38 no
P49950 Bcl2 Rattus norvegicus 38 no
Q6PSM0 Abcb1a Rattus norvegicus 38 no

Stratified review candidates

data/iep_review_candidates.tsv holds 4,807 not-yet-reviewed gene products sampled across the global term distribution (up to 3 per term, seeded for reproducibility) rather than only from the head of it, so the term strata the repo currently misses are represented.