g:Profiler - functional profiling of gene lists from large-scale experiments

J. Reimand, M. Kull, H. Peterson, J. Hansen, J. Vilo: g:Profiler -- a web-based toolset for functional profiling of gene lists from large-scale experiments (2007) NAR 35 W193-W200 [PDF]
J. Reimand, T. Arak, J. Vilo: g:Profiler -- a web server for functional interpretation of gene lists (2011 update) Nucleic Acids Research 2011; doi: 10.1093/nar/gkr378 [PDF]

[?] Organism

[?] Query (genes, proteins, probes, term)

[?] or Term ID:
	Run example

Options
[?] Significant only
[?] Ordered query
[?] No electronic GO annotations
[?] Chromosomal regions
[?] Hierarchical sorting
[?] Hierarchical filtering

[?] Output type

[?] Gene list as a stat. background
[?] User p-value
[?] Max size of functional category

[?] Numeric IDs treated as

[?] Significance threshold

[?] Statistical domain size

• Download g:Profiler data as GMT:
ENSG, name
• Run a random query

	[?] Inferred from experiment (IDA, IPI, IMP, IGI, IEP)
	Direct assay [IDA] / Mutant phenotype [IMP]
	Genetic interaction [IGI] / physical interaction [IPI]
	Expression pattern [IEP] / Sequence or structural similarity [ISS] / Genomic context [IGC]
	Traceable author [TAS] / Non-traceable author [NAS] / Inferred by curator [IC]
	Reviewed computational analysis [RCA] / Electronic annotation [IEA]
	Multiple GO evidence codes
	No data [ND] / Not annotated

	KEGG/REACTOME pathway

	[?] TRANSFAC regulatory motifs / [?] MicroCosm microRNA sites

	[?] CORUM protein complexes

	[?] Human disease genes from Human Phenotype Ontology
	[?] Sequence homologs of human disease genes, Human Phenotype Ontology

	[?] BioGRID protein-protein interaction networks
	BioGRID protein-protein interactions in gene query
	BioGRID protein-protein interactions in network neighborhood

>> g:Convert
Gene ID Converter

>> g:Orth
Orthology Search

>> g:Sorter
Expression Similarity Search

>> g:Cocoa
Compact Compare of Annotations

>> Static URL
Come back later

[?] Significantly enriched network of BioGRID interactions found. >> Show network

#INFO:	PARAMETERS: sort_by_structure = 1
#INFO:	PARAMETERS: user_thr = 1.00
#INFO:	PARAMETERS: significant = 1
#INFO:	PARAMETERS: organism = mmusculus
#INFO:	PARAMETERS: analytical = 1
#INFO:	User:  g:Profiler web interface
#INFO:	Host:  ronk1.at.mt.ut.ee
#INFO:	Time:  2013-5-24  13:13:54 
#INFO:	Effective domain size for REAC: 3118
#INFO:	Effective domain size for GO: 22302
#INFO:	Effective domain size for TF: 15264
#INFO:	Effective domain size for KEGG: 6972
#INFO:	Effective domain size for MI: 19507
#INFO:	Effective domain size for HP: 2461
#INFO:	
#INFO:	--- Gene names and descriptions
#INFO:	
#INFO:	QUERY:	GOSH:15582	CYP2R1	cytochrome P450, family 2, subfamily r, polypeptide 1 [Source:MGI Symbol;Acc:MGI:2449771]
#INFO:	QUERY:	GOSH:23084	SC4MOL	sterol-C4-methyl oxidase-like [Source:MGI Symbol;Acc:MGI:1913484]
#INFO:	QUERY:	GOSH:19570	HSD17B7	hydroxysteroid (17-beta) dehydrogenase 7 [Source:MGI Symbol;Acc:MGI:1330808]
#INFO:	QUERY:	GOSH:25243	DHCR7	7-dehydrocholesterol reductase [Source:MGI Symbol;Acc:MGI:1298378]
#INFO:	QUERY:	GOSH:32902	LIPA	lysosomal acid lipase A [Source:MGI Symbol;Acc:MGI:96789]
#INFO:	QUERY:	GOSH:32071	CYP27B1	cytochrome P450, family 27, subfamily b, polypeptide 1 [Source:MGI Symbol;Acc:MGI:1098274]
#INFO:	QUERY:	GOSH:14988	CYP24A1	cytochrome P450, family 24, subfamily a, polypeptide 1 [Source:MGI Symbol;Acc:MGI:88593]
#INFO:	QUERY:	GOSH:9329	LSS	lanosterol synthase [Source:MGI Symbol;Acc:MGI:1336155]
#INFO:	QUERY:	GOSH:31494	SOAT1	sterol O-acyltransferase 1 [Source:MGI Symbol;Acc:MGI:104665]
#INFO:	QUERY:	GOSH:30837	EBP	phenylalkylamine Ca2+ antagonist (emopamil) binding protein [Source:MGI Symbol;Acc:MGI:107822]
#INFO:	QUERY:	GOSH:16509	TM7SF2	transmembrane 7 superfamily member 2 [Source:MGI Symbol;Acc:MGI:1920416]
#INFO:	QUERY:	GOSH:9209	SOAT2	sterol O-acyltransferase 2 [Source:MGI Symbol;Acc:MGI:1332226]
#INFO:	QUERY:	GOSH:9718	DHCR24	24-dehydrocholesterol reductase [Source:MGI Symbol;Acc:MGI:1922004]
#INFO:	QUERY:	GOSH:34993	CYP51	cytochrome P450, family 51 [Source:MGI Symbol;Acc:MGI:106040]
#INFO:	QUERY:	GOSH:27885	CEL	carboxyl ester lipase [Source:MGI Symbol;Acc:MGI:88374]
#INFO:	QUERY:	GOSH:17879	NSDHL	NAD(P) dependent steroid dehydrogenase-like [Source:MGI Symbol;Acc:MGI:1099438]
#INFO:	QUERY:	GOSH:24701	SC5D	sterol-C5-desaturase (fungal ERG3, delta-5-desaturase) homolog (S. cerevisae) [Source:MGI Symbol;Acc:MGI:1353611]

g:Profiler 2005-2011
Jüri Reimand & Tambet Arak & Jaak Vilo @ BIIT Group, Institute of Computer Science, University of Tartu, Estonia.