Module name: nmf-uv

For all prey genes not used to define an NMF rank, it calculates what proportion are being assigned to a previously known localization. UV: unused validation

parameters	definition	default
basisMatrix	NMF basis matrix
goAnnotations	GO annotations in .gaf format
goHierarchy	GO hierarchy in .obo format
maxGenesPerRank	maximum number of genes to use per rank for enrichments	100
minRankValue	a prey must have an NMF value at or above this value to be used for enrichment	0.25
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 for RBD data points	uv-assessment.txt
withinRankMax	if a prey has an NMF value within this % of max in its non-primary rank, it can be used for enrichment	0.75

Example file formats

basisMatrix

variable,1,2,3
AAAS,0.0,0.18373784550412228,0.0
AAK1,0.13963834317658874,0.0,0.0
AAR2,0.0,0.016517285371126216,0.034697999230769466
AARS2,0.0,0.0,0.001598769548285137

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

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]

Output

• uv-assessment.txt