package
0.0.0-20220611144015-40008dcd7b35
Repository: https://github.com/knightjdr/cmgo.git
Documentation: pkg.go.dev
# README
Module name: assessment-countgo
Count the number of genes with a GO term specified by the supplied namespace.
| parameters | definition | default |
|---|---|---|
| genes | list of genes with assigned localizations | |
| goAnnotations | GO annotations in .gaf format | |
| namespace | GO namespace to use, one of BP, CC, MF | CC |
Example file formats
goAnnotations
!Documentation about this header can be found here: https://github.com/geneontology/go-site/blob/master/docs/gaf_validation.md
!
UniProtKB A0A024R161 DNAJC25-GNG10 GO:0003924 GO_REF:0000002 IEA InterPro:IPR001770 F Guanine nucleotide-binding protein subunit gamma DNAJC25-GNG10|hCG_1994888 protein taxon:9606 20190112 InterPro
UniProtKB A0A024R161 DNAJC25-GNG10 GO:0007186 GO_REF:0000002 IEA InterPro:IPR001770|InterPro:IPR015898|InterPro:IPR036284 P Guanine nucleotide-binding protein subunit gamma DNAJC25-GNG10|hCG_1994888 protein taxon:9606 20190112 InterPro
UniProtKB Q9BUL8 PDCD10 GO:0000139 GO_REF:0000039 IEA UniProtKB-SubCell:SL-0134 C Programmed cell death protein 10 PDCD10|CCM3|TFAR15 protein taxon:9606 20190112 UniProt
UniProtKB Q9BUL8 PDCD10 GO:0001525 GO_REF:0000037 IEA UniProtKB-KW:KW-0037 P Programmed cell death protein 10 PDCD10|CCM3|TFAR15 protein taxon:9606 20190112 UniProt
UniProtKB Q9BUL8 PDCD10 GO:0005515 PMID:16189514 IPI UniProtKB:O00506 F Programmed cell death protein 10 PDCD10|CCM3|TFAR15 protein taxon:9606 20190113 IntAct
UniProtKB Q9BUL8 PDCD10 GO:0005515 PMID:16189514 IPI UniProtKB:Q9Y6E0 F Programmed cell death protein 10 PDCD10|CCM3|TFAR15 protein taxon:9606 20190113 IntAct
UniProtKB Q9BUL9 RPP25 GO:0001682 Reactome:R-HSA-5696810 TAS P Ribonuclease P protein subunit p25 RPP25 protein taxon:9606 20151024 Reactome
UniProtKB Q9BUL9 RPP25 GO:0003723 PMID:22658674 HDA F Ribonuclease P protein subunit p25 RPP25 protein taxon:9606 20140203 UniProt
UniProtKB Q9BUL9 RPP25 GO:0005515 PMID:15096576 IPI UniProtKB:O95707 F Ribonuclease P protein subunit p25 RPP25 protein taxon:9606 20190113 IntAct
UniProtKB Q9BUL9 RPP25 GO:0005515 PMID:21044950 IPI UniProtKB:Q9NYB0 F Ribonuclease P protein subunit p25 RPP25 protein taxon:9606 20190113 IntAct
UniProtKB Q9BUL9 RPP25 GO:0005654 GO_REF:0000052 IDA C Ribonuclease P protein subunit p25 RPP25 protein taxon:9606 20141106 HPA
genes
File with a header and genes names in the first column.
# Functions
Sum counts the number of supplied genes with at least one known GO term in the supplied namespace.