Module name: assessment-prediction

Assign a prediction score for every prey localized by NMF or SAFE

parameters	definition	default
baitExpected	expected bait localizations
compartmentsText	text-mining score from Comportments DB
domainsPerCompartment	file with a list of domains for each NMR rank or SAFE domain
domainsPerGene	file with a list of domains for each gene
fdr	FDR for significant prey in SAINT file
fractionation	predictions from fractionation studies of Christoforou and Itzhak
goHierarchy	GO hierarchy in .obo format
hpa	human protein atlas predictions
outFile	output file	prediction-score.txt
predictions	file with localization predictions by NMF rank or SAFE domain
predictionSummary	summary information for NMF or SAFE ranks
predictionType	type of prediction: NMF or SAFE	nmf
saint	SAINT file

| uniprot | UniProt file in .dat format | |

Example file formats

baitExpected

id	bait	term	GO_ID
1	AARS2	mitochondrial matrix	GO:0005759
2	ACBD5	peroxisome	GO:0005777
3	ACTB	actin cytoskeleton	GO:0015629

compartmentsText

ENSP00000255087	MTL5	GO:0042645	Mitochondrial nucleoid	1.010	0.505	
ENSP00000255087	MTL5	GO:0000229	Cytoplasmic chromosome	1.009	0.504	
ENSP00000255087	MTL5	GO:0045495	Pole plasm	1.004	0.502	
ENSP00000255108	DPH2	GO:0005840	Ribosome	3.332	1.666	
ENSP00000255108	DPH2	GO:1990904	Ribonucleoprotein complex	3.077	1.538

domainsPerCompartment

rank	term	matched	background_size	fold enrichment	pvalue	adj. pvalue	bhfdr	genes
1	PDZ	23	48	8.906	1.62980740014973e-13	4.27009538839229e-11	3.81679389312977e-05	AFDN,CASK
1	FERM_C	12	17	13.120	2.1798629399977e-12	2.85562045139698e-10	7.63358778625954e-05	EPB41,EPB41L5

domainsPerGene

#<seq id> <alignment start> <alignment end> <envelope start> <envelope end> <hmm acc> <hmm name> <type> <hmm start> <hmm end> <hmm length> <bit score> <E-value> <clan>
O95863	153	176	153	177	PF13912	zf-C2H2_6	PfamLive::Result::SequenceOntology=HASH(0x108198b8)	1	24	27	20.50	0.9	CL0361
O95863	208	230	208	230	PF00096	zf-C2H2	PfamLive::Result::SequenceOntology=HASH(0x89b8a80)	1	23	23	26.70	0.013	CL0361
O95863	181	202	180	202	PF00096	zf-C2H2	PfamLive::Result::SequenceOntology=HASH(0x89b8a80)	2	23	23	23.40	0.14	CL0361

fractionation

gene	localization Christoforou	localization Itzhak	ID Christoforou	ID Itzhak	combined
AARS	Cytosol	Mostly Cytosolic	GO:0005829	GO:0005829	GO:0005829
AARS2	Mitochondrion	Mitochondrion Matrix	GO:0005739	GO:0005759	GO:0005739;GO:0005759
AARSD1	Cytosol	Mostly Cytosolic	GO:0005829	GO:0005829	GO:0005829

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

hpa

gene	terms	go_id
TSPAN6	Cytosol	GO:0005829
SCYL3	Microtubules;Nuclear bodies	GO:0015630;GO:0016604
C1orf112	Mitochondria	GO:0005739
FGR	Aggresome;Plasma membrane	GO:0016235;GO:0005886
CFH	Vesicles	GO:0043231

predictions

NMF

gene	rank	score
AAAS	13	0.3326865	
AAK1	5	0.1396383	
AAR2	19	0.034698	
AARS2	6	0.2251458	
AASDH	2	0.09391108

SAFE

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

predictionSummary

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

prediction-score.txt: output prediction score components for each prey