nmfsafe

README

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

Example file formats

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

Documentation

Overview

Package nmfsafe checks NMF and SAFE localizations for agreement.

Index

• func Concordance(fileOptions map[string]interface{})

Functions

func Concordance

func Concordance(fileOptions map[string]interface{})

Concordance checks NMF and SAFE localizations for agreement.