Table of contents

Summary

GAF summary

Found 1458 annotations in 1463 lines.

GAF Validation Summary Errors are reported first.

For rule GO_AR:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014) Valid GO term ID, there are 2 violations with type Error.

For rule GO_AR:0000007 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000007) IPI should not be used with catalytic activity molecular function terms, there is one violation with type Warning.

For rule GO_AR:0000008 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000008) No annotations should be made to uninformative high level terms, there are 23 violations with type Warning.

For rule GO_AR:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014) Valid GO term ID, there are 2 violations with type Warning.

For rule GO_AR:0000016 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000016) IC annotations require a With/From GO ID, there is one violation with type Warning.

GAF Prediction Summary

Found 107 predictions, see prediction file for details.

Used Ontology Summary

go/extensions/go-gaf

Report

SUMMARY

STATISTICS

MESSAGES

WARNING

OWLTools check

#Line number RuleID ViolationType Message Line
#------------
#------------
# Validation for #1458 annotations in 1463 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000014 Valid GO term ID Error count: 2
100 GO_AR:0000014 Error The id 'GO:0000988' in the annotation is an obsolete class SGN 8326 HSFA2 GO:0000988 PMID:19491106 IDA F heat stress transcription factor A2 gene taxon:4081 20120224 SGN
1453 GO_AR:0000014 Error The id 'GO:0042965' in the annotation is an obsolete class SGN 43099 SlGRX1 GO:0042965 PMID:20862491 IDA P glutaredoxin gene gene taxon:4081 20101210 SGN
#------------
# GO_AR:0000007 IPI should not be used with catalytic activity molecular function terms Warning count: 1
80 GO_AR:0000007 Warning IPI should not be used with catalytic activity molecular function terms SGN 5257 pmt GO:0030750 PMID:17221359 IPI NCBI_gi:86438859 F putrescine N-methyltransferase Solyc06g053510 gene taxon:4081 20090625 SGN
#------------
# GO_AR:0000008 No annotations should be made to uninformative high level terms Warning count: 23
8 GO_AR:0000008 Warning Do not annotate to: GO:0044428 'nuclear part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 364 c14 GO:0044428 PMID:11444695 IDA C cysteine protease CYP1 C14|tdi-65|Solyc12g088670 gene taxon:4081 20090612 SGN
9 GO_AR:0000008 Warning Do not annotate to: GO:0044434 'chloroplast part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 364 c14 GO:0044434 PMID:11444695 IDA C cysteine protease CYP1 C14|tdi-65|Solyc12g088670 gene taxon:4081 20090612 SGN
16 GO_AR:0000008 Warning Do not annotate to: GO:0044459 'plasma membrane part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 1027 LeST1-1 GO:0044459 PMID:12937983 IDA C sulfate transporter 1 THT1-3|THT7-1|THT1-4|Solyc10g047170 gene taxon:4081 20090929 SGN
27 GO_AR:0000008 Warning Do not annotate to: GO:0044459 'plasma membrane part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 5291 amt1 GO:0044459 PMID:8755617 IDA C AMT1 Solyc09g090730 gene taxon:4081 20090929 SGN
28 GO_AR:0000008 Warning Do not annotate to: GO:0044459 'plasma membrane part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 5389 LeST1-2 GO:0044459 PMID:12937983 IDA C sulfate transporter 2 AF347614|Solyc12g056930 gene taxon:4081 20090929 SGN
39 GO_AR:0000008 Warning Do not annotate to: GO:0044434 'chloroplast part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 17699 SlBCAT4 GO:0044434 PMID:20435740 IDA C SlBCAT4 Solyc03g043880 gene taxon:4081 20120131 SGN
41 GO_AR:0000008 Warning Do not annotate to: GO:0044429 'mitochondrial part' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate SGN 110964 SlBCAT2 GO:0044429 PMID:20435740 IDA C SlBCAT2 Solyc07g021630 gene taxon:4081 20120130 SGN
100 GO_AR:0000008 Warning Do not annotate to: GO:0000988 'obsolete transcription factor activity, protein binding' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 8326 HSFA2 GO:0000988 PMID:19491106 IDA F heat stress transcription factor A2 gene taxon:4081 20120224 SGN
297 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 68 SlIAA3 GO:0006950 PMID:22314799 IDA P auxin-regulated IAA3 LeIAA3|IAA3|Solyc09g065850 gene taxon:4081 20141120 SGN
329 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 463 e GO:0006950 PMID:22314799 IEP P entire b|SlIAA9|iaa9|LeIAA4|IAA4|ctd1|Solyc04g076850|SlIAA4 gene taxon:4081 20141120 SGN
434 GO_AR:0000008 Warning Do not annotate to: GO:0009628 'response to abiotic stimulus' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 4506 Asr2 GO:0009628 PMID:17602312 IEP P Abscicic acid stress ripening 2 Solyc04g071580 gene taxon:4081 20080215 SGN
543 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 9403 SlMAPKKK1 GO:0006950 PMID:25036993 IDA P MAP kinase kinase kinase 1 Solyc01g005030|MAPKKK1 gene taxon:4081 20141103 SGN
862 GO_AR:0000008 Warning Do not annotate to: GO:0009628 'response to abiotic stimulus' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 20062 iaa14 GO:0009628 PMID:22314799 IDA P auxin-regulated IAA14 Solyc03g121060|SlIAA14 gene taxon:4081 20141121 SGN
901 GO_AR:0000008 Warning Do not annotate to: GO:0009628 'response to abiotic stimulus' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 22083 Asr_2 GO:0009628 PMID:17602312 IEP P Abscicic acid stress ripening 2 Solyc04g071580|Asr2 gene taxon:4081 20120509 SGN
1004 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 26635 SlC3H43 GO:0006950 PMID:24870401 ISS P Zinc finger transcription factor 43 Solyc06g054620|C3H43 gene taxon:4081 20150304 SGN
1047 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 27917 SlC3H48 GO:0006950 PMID:24870401 ISS P Zinc finger transcription factor 48 24870401|C3H48|Solyc06g082010 gene taxon:4081 20150304 SGN
1068 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 28803 SlIAA20 GO:0006950 PMID:22314799 IDA P auxin-regulated IAA20 SlIAA20|iaa20|Solyc07g019450 gene taxon:4081 20141121 SGN
1112 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 29921 SlC3H50 GO:0006950 PMID:24870401 ISS P Zinc finger transcription factor 50 Solyc07g053750|C3H50 gene taxon:4081 20150304 SGN
1226 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 35249 SlIAA1 GO:0006950 PMID:22314799 IDA P auxin-regulated IAA1 IAA1|Solyc09g083280 gene taxon:4081 20141124 SGN
1378 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 40630 SlMAPKKK83 GO:0006950 PMID:25036993 IEP P MAP kinase kinase kinase 83 MAPKKK83|Solyc12g005360 gene taxon:4081 20141111 SGN
1391 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 40851 SlC3H73 GO:0006950 PMID:24870401 ISS P Zinc finger transcription factor 73 Solyc12g008660|C3H73 gene taxon:4081 20150304 SGN
1401 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 40914 SlMAPKKK84 GO:0006950 PMID:25036993 IEP P MAP kinase kinase kinase 84 MAPKKK84|Solyc12g009340 gene taxon:4081 20141111 SGN
1439 GO_AR:0000008 Warning Do not annotate to: GO:0006950 'response to stress' The term is considered to high level, as marked via the subset tag: gocheck_do_not_manually_annotate SGN 42691 SlC3H80 GO:0006950 PMID:24870401 ISS P Zinc finger transcription factor 80 C3H80|Solyc12g089260 gene taxon:4081 20150304 SGN
#------------
# GO_AR:0000014 Valid GO term ID Warning count: 2
52 GO_AR:0000014 Warning The id 'GO:0004872' in the annotation is an alternate id for: GO:0038023 SGN 662 Gr GO:0004872 PMID:15834010 IMP F green ripe gr|DQ372895|Solyc01g104340 gene taxon:4081 20071005 SGN
66 GO_AR:0000014 Warning The id 'GO:0004872' in the annotation is an alternate id for: GO:0038023 SGN 1046 Nr2 GO:0004872 PMID:15834010 IMP F Never ripe-2 Nr-2|Never-ripe|Solyc09g075440 gene taxon:4081 20071005 SGN
#------------
# GO_AR:0000016 IC annotations require a With/From GO ID Warning count: 1
493 GO_AR:0000016 Warning IC annotations require a With/From GO ID SGN 5583 tg1 GO:0016120 SGN_ref:861 IC P test gene tg2|tg gene taxon:4081 20121115 SGN
#------------

Predictions

GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0045552 dihydrokaempferol 4-reductase activity ISS
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0045544 gibberellin 20-oxidase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0006508 proteolysis AnnotationPropagation P GO:0008234 cysteine-type peptidase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0010466 negative regulation of peptidase activity AnnotationPropagation P GO:0030414 peptidase inhibitor activity IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0098869 cellular oxidant detoxification AnnotationPropagation P GO:0016209 antioxidant activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0006355 regulation of transcription, DNA-templated AnnotationPropagation P GO:0003700 DNA-binding transcription factor activity IDA
GO:0006468 protein phosphorylation AnnotationPropagation P GO:0004672 protein kinase activity IDA
GO:0006355 regulation of transcription, DNA-templated AnnotationPropagation P GO:0003700 DNA-binding transcription factor activity IMP
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0045544 gibberellin 20-oxidase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0045544 gibberellin 20-oxidase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0006355 regulation of transcription, DNA-templated AnnotationPropagation P GO:0003700 DNA-binding transcription factor activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0006355 regulation of transcription, DNA-templated AnnotationPropagation P GO:0003700 DNA-binding transcription factor activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0010951 negative regulation of endopeptidase activity AnnotationPropagation P GO:0004869 cysteine-type endopeptidase inhibitor activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0000165 MAPK cascade AnnotationPropagation P GO:0004707 MAP kinase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0004784 superoxide dismutase activity IDA
GO:0019430 removal of superoxide radicals AnnotationPropagation P GO:0004784 superoxide dismutase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0033744 L-methionine:thioredoxin-disulfide S-oxidoreductase activity IDA
GO:0032259 methylation AnnotationPropagation P GO:0016206 catechol O-methyltransferase activity IDA
GO:0005622 intracellular AnnotationPropagation C GO:0000165 MAPK cascade IDA

Predictions (experimental)