Module name: nmf-v-safe
Check concordance between NMF and SAFE localizations.
parameters |
definition |
default |
goAnnotations |
GO annotations in .gaf format |
|
goHierarchy |
GO hierarchy in .obo format |
|
namespace |
GO namespace to use, one of BP, CC, MF |
CC |
nmfLocalization |
Text file with assigned NMF rank and score for each gene |
|
nmfSummary |
NMF rank summary file |
|
outFile |
output file name |
concordance.txt |
outSummaryFile |
file with summary statistics |
summary.txt |
safeLocalization |
Node properties file output from SAFE |
|
safeSummary |
SAFE domain summary file |
|
annotationsFile
!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
goHierarchy
[Term]
id: GO:0005652
name: nuclear lamina
namespace: cellular_component
def: "The fibrous, electron-dense layer lying on the nucleoplasmic side of the inner membrane of a cell nucleus." [ISBN:0198506732, ISBN:0716731363]
xref: NIF_Subcellular:sao1455996588
xref: Wikipedia:Nuclear_lamina
is_a: GO:0044428 ! nuclear part
relationship: part_of GO:0034399 ! nuclear periphery
[Term]
id: GO:0005654
name: nucleoplasm
namespace: cellular_component
def: "That part of the nuclear content other than the chromosomes or the nucleolus." [GOC:ma, ISBN:0124325653]
subset: goslim_chembl
subset: goslim_generic
subset: goslim_plant
xref: NIF_Subcellular:sao661522542
xref: Wikipedia:Nucleoplasm
is_a: GO:0044428 ! nuclear part
relationship: part_of GO:0031981 ! nuclear lumen
nmfLocalization
gene rank score
AAAS 13 0.3326865
AAK1 5 0.1396383
AAR2 19 0.034698
AARS2 6 0.2251458
AASDH 2 0.09391108
nmfSummary and safeSummary
rank term displayname go synonyms ic
1 [cell junction] [cell junction] [GO:0030054] [] [1.166]
2 [chromosome] [chromatin] [GO:0005694] "[[chromatid, interphase chromosome, prophase chromosome]]" [1.256]
safeLocalization
##
## This file lists the properties of all nodes in the network.
##
Node label Node label ORF Domain (predominant) Neighborhood score [max=1, min=0] (predominant) Total number of enriched domains Number of enriched attributes per domain
VAMP3 VAMP3 20 0.600 1 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0,0
SNAP29 SNAP29 1 0.263 0 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
CDCA3 CDCA3 20 1.000 1 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,61,0,0,0,0
Output
- txt file: for each gene list NMF and SAFE term, is it known, and whether they agree
- txt file with summary statistics