NOT annotation usage: results

Species: human, rat, ARATH, SCHPO

NOT annotation usage: results

Generated by analyze_not_usage.py; do not edit by hand.

By aspect

Aspect NOT rows %
F 4664 43.9
P 3857 36.3
C 2101 19.8

By relation

Relation NOT rows %
enables 4637 43.7
involved_in 3396 32.0
located_in 1541 14.5
acts_upstream_of_or_within 453 4.3
is_active_in 419 3.9
part_of 113 1.1
colocalizes_with 28 0.3
contributes_to 27 0.3
acts_upstream_of_or_within_negative_effect 4 0.0
acts_upstream_of 2 0.0
acts_upstream_of_or_within_positive_effect 2 0.0

By evidence code

Evidence NOT rows %
IBA 2590 24.4
IDA 2481 23.4
ISO 1679 15.8
IMP 1091 10.3
ISS 906 8.5
IKR 701 6.6
RCA 627 5.9
IEP 169 1.6
TAS 121 1.1
IGI 100 0.9
NAS 49 0.5
EXP 35 0.3
IPI 32 0.3
ISA 23 0.2
ISM 7 0.1
IC 5 0.0
HDA 4 0.0
IGC 2 0.0

By assigning group

Assigned by NOT rows %
GO_Central 2604 24.5
UniProt 2545 24.0
RGD 1640 15.4
FlyBase 1186 11.2
TAIR 998 9.4
MGI 330 3.1
ZFIN 231 2.2
BHF-UCL 231 2.2
PomBase 218 2.1
AgBase 202 1.9
GeneDB 78 0.7
ARUK-UCL 62 0.6
MTBBASE 57 0.5
CAFA 53 0.5
HGNC-UCL 51 0.5
ParkinsonsUK-UCL 45 0.4
CGD 32 0.3
dictyBase 16 0.2
WB 13 0.1
DFLAT 9 0.1
AspGD 8 0.1
EcoliWiki 5 0.0
HGNC 3 0.0
PHI-base 2 0.0
Roslin_Institute 1 0.0
CACAO 1 0.0
JaponicusDB 1 0.0

By term category

Category NOT rows %
catalytic activity 3405 32.1
cellular component 2101 19.8
metabolic process 1010 9.5
regulation of biological process 796 7.5
binding (other) 672 6.3
response to stimulus (other) 490 4.6
other BP 430 4.0
developmental process 423 4.0
transporter activity 329 3.1
localization 293 2.8
defense/immune response 234 2.2
signaling 181 1.7
other MF 128 1.2
molecular transducer activity 69 0.6
transcription regulator activity 59 0.6
protein binding (bare) 2 0.0

Evidence code within each category

Category Rows Top evidence codes
catalytic activity 3405 IBA 1336, IDA 752, IKR 608, ISS 291, ISO 267
cellular component 2101 RCA 627, IDA 593, IBA 399, ISO 331, ISS 107
metabolic process 1010 IBA 584, IMP 104, IDA 102, ISO 84, ISS 68
regulation of biological process 796 ISO 264, IMP 236, IDA 142, ISS 74, IBA 40
binding (other) 672 IDA 281, ISO 167, ISS 100, IBA 58, IPI 23
response to stimulus (other) 490 IEP 138, IMP 103, ISO 72, IDA 47, IBA 40
other BP 430 IMP 151, ISO 117, IDA 89, ISS 40, IBA 14
developmental process 423 IMP 245, ISO 82, ISS 36, IEP 15, IGI 13
transporter activity 329 IDA 136, ISO 90, ISS 61, IMP 18, IBA 12
localization 293 IDA 89, ISO 83, IMP 62, ISS 52, IEP 3
defense/immune response 234 IDA 140, IMP 49, ISO 34, ISS 7, IEP 2
signaling 181 ISO 50, IBA 40, IMP 37, IDA 26, IGI 12
other MF 128 IDA 40, IKR 32, ISO 21, IBA 12, ISS 7
molecular transducer activity 69 IDA 26, ISS 22, ISO 13, IKR 3, TAS 3
transcription regulator activity 59 IBA 45, IDA 9, ISO 4, IMP 1
protein binding (bare) 2 IPI 2

'Response to' NOTs (excluding signaling and defense/immune)

490 NOT rows are to descendants of GO:0050896 response to stimulus that are not signaling pathways or defense/immune responses: mostly responses to chemicals, abiotic stimuli and endogenous signals.

Evidence rows %
IEP 138 28.2
IMP 103 21.0
ISO 72 14.7
IDA 47 9.6
IBA 40 8.2
ISS 33 6.7
IGI 28 5.7
TAS 13 2.7
EXP 6 1.2
NAS 5 1.0
ISA 3 0.6
IKR 2 0.4

Most frequent terms:

GO term Label Rows
GO:0019740 nitrogen utilization 38
GO:0009611 response to wounding 17
GO:0009408 response to heat 17
GO:0006281 DNA repair 15
GO:0009737 response to abscisic acid 15
GO:0009739 response to gibberellin 12
GO:0009409 response to cold 11
GO:0031848 protection from non-homologous end joining at telomere 11
GO:0009651 response to salt stress 9
GO:0021834 chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration 9
GO:0070542 response to fatty acid 9
GO:0001964 startle response 9
GO:0006805 xenobiotic metabolic process 8
GO:0009751 response to salicylic acid 8
GO:0009733 response to auxin 8

NOTs supported only by expression pattern (IEP)

169 NOT rows use IEP. An expression measurement cannot show that a gene product lacks a function, so these are the clearest misuse of the qualifier.

Assigned by rows %
AgBase 65 38.5
UniProt 44 26.0
TAIR 33 19.5
FlyBase 17 10.1
RGD 6 3.6
BHF-UCL 3 1.8
MTBBASE 1 0.6
Category rows %
response to stimulus (other) 138 81.7
developmental process 15 8.9
regulation of biological process 5 3.0
localization 3 1.8
other BP 3 1.8
signaling 3 1.8
defense/immune response 2 1.2

Alignment with UniProt CAUTION notes

Counts are per reviewed (Swiss-Prot) protein carrying at least one NOT annotation. 'Negative-activity CAUTION' means the CAUTION text matches a loss-of-activity pattern (lacks, inactive, pseudo, no ... activity, and similar).

Protein set Any CAUTION Negative-activity CAUTION
Reviewed proteins with any NOT 663/4226 (15.7%) 404/4226 (9.6%)
... with a NOT to a molecular function 496/1838 (27.0%) 358/1838 (19.5%)
... with NOTs only to BP/CC 167/2388 (7.0%) 46/2388 (1.9%)

How this repo's reviews treated negated annotations

270 negated rows across 174 reviewed genes.

Action rows %
ACCEPT 223 82.6
UNDECIDED 20 7.4
KEEP_AS_NON_CORE 16 5.9
REMOVE 8 3.0
MARK_AS_OVER_ANNOTATED 3 1.1
Evidence rows %
IDA 130 48.1
IMP 61 22.6
IBA 17 6.3
IKR 14 5.2
ISS 11 4.1
TAS 9 3.3
ISO 8 3.0
IGI 7 2.6
NAS 3 1.1
EXP 3 1.1
RCA 2 0.7
IEP 2 0.7
IPI 2 0.7
IC 1 0.4

Action by term category

Category Rows Actions
catalytic activity 74 ACCEPT 65, UNDECIDED 5, KEEP_AS_NON_CORE 4
regulation of biological process 45 ACCEPT 36, UNDECIDED 6, REMOVE 2, KEEP_AS_NON_CORE 1
cellular component 36 ACCEPT 29, KEEP_AS_NON_CORE 4, REMOVE 3
metabolic process 26 ACCEPT 22, KEEP_AS_NON_CORE 2, UNDECIDED 2
binding (other) 23 ACCEPT 22, MARK_AS_OVER_ANNOTATED 1
other BP 13 ACCEPT 11, MARK_AS_OVER_ANNOTATED 1, KEEP_AS_NON_CORE 1
transporter activity 13 ACCEPT 9, UNDECIDED 4
localization 11 ACCEPT 7, UNDECIDED 2, REMOVE 1, KEEP_AS_NON_CORE 1
response to stimulus (other) 8 KEEP_AS_NON_CORE 3, ACCEPT 3, REMOVE 2
developmental process 6 ACCEPT 4, MARK_AS_OVER_ANNOTATED 1, UNDECIDED 1
signaling 5 ACCEPT 5
other MF 5 ACCEPT 5
unknown 4 ACCEPT 4
defense/immune response 1 ACCEPT 1

Worklist: reviewed NOTs to non-defense 'response to' terms or with IEP evidence

Organism Gene GO term Label Evidence Current action
ARATH CLV3 GO:0002221 pattern recognition receptor signaling pathway IEP ACCEPT
ARATH GID1A GO:0009739 response to gibberellin IGI KEEP_AS_NON_CORE
SCHPO chk1 GO:0006281 DNA repair EXP ACCEPT
human AGR2 GO:0034976 response to endoplasmic reticulum stress IMP REMOVE
human CRY2 GO:0000719 photoreactive repair IDA ACCEPT
human FGFR4 GO:1903412 response to bile acid IMP REMOVE
human GCH1 GO:0032496 response to lipopolysaccharide IEP KEEP_AS_NON_CORE
human HSPA6 GO:0070370 cellular heat acclimation IMP ACCEPT
rat Ghr GO:0046898 response to cycloheximide ISO KEEP_AS_NON_CORE