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g:Profiler - functional profiling of gene lists from large-scale experiments
 g:GOSt Gene Group Functional Profiling
 g:Cocoa Compact Compare of Annotations
 g:Convert Gene ID Converter
 g:Sorter Expression Similarity Search
 g:Orth Orthology search
Welcome! About Contact
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]
[?] Organism

[?] Query (genes, proteins, probes)

[?] or Chromosome region
[?]Significance threshold
[?] g:SCS threshold
[?] Bonferroni correction
[?] Benjamini-Hochberg FDR
[?] Statistical domain size



[?] or Term ID:
Output options
[?] Significant only
[?] Hierarchical sorting
[?]  User p-value
[?] Output type

Input options
[?] Ordered query
[?] Ignore unknown entries
[?] Numeric IDs treated as
Z [?] Inferred from experiment (IDA, IPI, IMP, IGI, IEP)
D M Direct assay [IDA] / Mutant phenotype [IMP]
G P Genetic interaction [IGI] / physical interaction [IPI]
X S Y Expression pattern [IEP] / Sequence or structural similarity [ISS] / Genomic context [IGC]
A a C Traceable author [TAS] / Non-traceable author [NAS] / Inferred by curator [IC]
E e Reviewed computational analysis [RCA] / Electronic annotation [IEA]
# Multiple GO evidence codes
O ? No data [ND] / Not annotated
k r KEGG/REACTOME pathway
m mi [?] TRANSFAC regulatory motifs / miRBase microRNA sites

News
16.03.2010 -- g:Profiler now includes Ensembl Genomes (Fungi, Metazoa and Plants) and has been updated to Ensembl release 57 and Ensembl Genomes release 4. Three new species are available: Turkey (Ensembl, Meleagris gallopavo), bread mould (EG Fungi, Neurospora crassa) and body louse (EG Metazoa, Pediculus humanus).
01.03.2010 -- We would like to announce a special testing release of g:Profiler Genomes (http://biit.cs.ut.ee/gprofiler_beta/) with the support of 82 species from Ensembl, Ensembl Fungi, Ensembl Plants and Ensembl Metazoa. This release includes previously uncovered model organisms such as Arabidopsis thaliana, Schizosaccharomyces pombe, 12 flies, etc.
20.10.2009 -- The new g:Profiler update incorporates data from Ensembl 56 and Reactome 30.
18.09.2009 -- The new g:Profiler update incorporates data from Ensembl 55 and Reactome 29. New features include querying by chromosome region and additional support for fully numeric IDs. Evidence codes and colors have been updated to include the new experimental code EXP.
25.05.2009 -- The new g:Profiler data update incorporates Ensembl 54 and Reactome 28.
22.03.2009 -- The new g:Profiler data update incorporates Ensembl 53 and Reactome 27.
06.05.2008 -- GraphWeb, a sister tool of g:Profiler, is now published in NAR Web Server Issue (Advance Access). J. Reimand, L. Tooming, H. Peterson, P. Adler & J. Vilo (2008): GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. doi:10.1093/nar/gkn230.
14.02.2008 -- KEGGanim, a sister tool of g:Profiler, was published in Bioinformatics. P. Adler, J. Reimand, J. Janes, R. Kolde, H. Peterson & J. Vilo (2008): KEGGanim: pathway animations for high-throughput data. Bioinformatics 24, 588-590.

Welcome to g:GOSt!


g:GOSt retrieves most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs to a user-specified group of genes, proteins or microarray probes. g:GOSt also allows analysis of ranked or ordered lists of genes, visual browsing of GO graph structure, interactive visualisation of retrieved results, and many other features. Multiple testing corrections are applied to extract only statistically important results.

g:GOSt quick-start guide:
  1. Select an organism from top left drop-down menu.
  2. Type or paste your genes, proteins or probes of interest into the query textbox.
  3. Click the button "g:Profile!" to initiate calculation.
Example queries:
  • Query1 - 30 Affymetrix probes sorted by expression similarity to INHBA, a member of human TGF-beta signalling pathway.
  • Query2 - Mouse genes mapping to KEGG steroid biosynthesis pathway.
  • Query3 - textual list of all known annotations of human gene PAX6.
Tips and tricks:
  • If your query did not give any results, disable Significant only checkbox in output options.
  • Activate Ordered query checkbox to treat the input as an ordered list. g:Profiler then finds the best-matching sublist for every term.
  • Select Textual from output menu to get a tab-separated textual result.
  • If query results in a lot of terms, g:Profiler will give textual output instead of PNG image.
  • Links like [?] provide help.
Help and support topics:







g:Profiler 2005-2008
Jüri Reimand & Jaak Vilo @ BIIT Group, Institute of Computer Science, University of Tartu.