Bioinformatics. 2004 Jun 12;20(9):1464-5. Epub 2004 Feb 12.

GOstat: find statistically overrepresented Gene Ontologies within a group of genes.

Source

Walter and Eliza Hall Institute of medical Research, 1G Royal Parade, Parkville, Vic 3050, Australia. beissbarth@wehi.edu.au

Abstract

SUMMARY: Modern experimental techniques, as for example DNA microarrays, as a result usually produce a long list of genes, which are potentially interesting in the analyzed process. In order to gain biological understanding from this type of data, it is necessary to analyze the functional annotations of all genes in this list. The Gene-Ontology (GO) database provides a useful tool to annotate and analyze the functions of a large number of genes. Here, we introduce a tool that utilizes this information to obtain an understanding of which annotations are typical for the analyzed list of genes. This program automatically obtains the GO annotations from a database and generates statistics of which annotations are overrepresented in the analyzed list of genes. This results in a list of GO terms sorted by their specificity. AVAILABILITY: Our program GOstat is accessible via the Internet at http://gostat.wehi.edu.au

PMID:: 14962934; [PubMed - indexed for MEDLINE]

Free full text

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Libraries

LinkOut Holdings

Supplemental Content

Related citations

NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis. [Bioinformatics. 2004]
NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis.
Cheng J, Sun S, Tracy A, Hubbell E, Morris J, Valmeekam V, Kimbrough A, Cline MS, Liu G, Shigeta R, et al. Bioinformatics. 2004 Jun 12; 20(9):1462-3. Epub 2004 Feb 12.
Review Interpreting experimental results using gene ontologies. [Methods Enzymol. 2006]
Review Interpreting experimental results using gene ontologies.
Beissbarth T. Methods Enzymol. 2006; 411:340-52.
GObar: a gene ontology based analysis and visualization tool for gene sets. [BMC Bioinformatics. 2005]
GObar: a gene ontology based analysis and visualization tool for gene sets.
Lee JS, Katari G, Sachidanandam R. BMC Bioinformatics. 2005 Jul 25; 6:189. Epub 2005 Jul 25.
CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology. [Bioinformatics. 2004]
CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology.
Shah NH, Fedoroff NV. Bioinformatics. 2004 May 1; 20(7):1196-7. Epub 2004 Feb 5.
Review Get ready to GO! A biologist's guide to the Gene Ontology. [Brief Bioinform. 2005]
Review Get ready to GO! A biologist's guide to the Gene Ontology.
Lomax J. Brief Bioinform. 2005 Sep; 6(3):298-304.

See reviews... See all...

Cited by over 100 PubMed Central articles

Single sample expression-anchored mechanisms predict survival in head and neck cancer. [PLoS Comput Biol. 2012]
Single sample expression-anchored mechanisms predict survival in head and neck cancer.
Yang X, Regan K, Huang Y, Zhang Q, Li J, Seiwert TY, Cohen EE, Xing HR, Lussier YA. PLoS Comput Biol. 2012 Jan; 8(1):e1002350. Epub 2012 Jan 26.
Computational prediction of host-parasite protein interactions between P. falciparum and H. sapiens. [PLoS One. 2011]
Computational prediction of host-parasite protein interactions between P. falciparum and H. sapiens.
Wuchty S. PLoS One. 2011; 6(11):e26960. Epub 2011 Nov 17.
Hesperidin displays relevant role in the nutrigenomic effect of orange juice on blood leukocytes in human volunteers: a randomized controlled cross-over study. [PLoS One. 2011]
Hesperidin displays relevant role in the nutrigenomic effect of orange juice on blood leukocytes in human volunteers: a randomized controlled cross-over study.
Milenkovic D, Deval C, Dubray C, Mazur A, Morand C. PLoS One. 2011; 6(11):e26669. Epub 2011 Nov 16.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Compound (MeSH Keyword)
PubChem chemical compound records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

GOstat: find statistically overrepresented Gene Ontologies within a group of gen...
GOstat: find statistically overrepresented Gene Ontologies within a group of genes.
Bioinformatics. 2004 Jun 12 ;20(9):1464-5. Epub 2004 Feb 12 .

PubMed
Being in the right location at the right time.
Being in the right location at the right time.
Genome Biol. 2001 ;2(9):REVIEWS1024. Epub 2001 Aug 29 .

PubMed
Divorcing ARF and p53: an unsettled case.
Divorcing ARF and p53: an unsettled case.
Nat Rev Cancer. 2006 Sep ;6(9):663-73. Epub 2006 Aug 17 .

PubMed
Global gene expression profiling in Escherichia coli K12. The effects of integra...
Global gene expression profiling in Escherichia coli K12. The effects of integration host factor.
J Biol Chem. 2000 Sep 22 ;275(38):29672-84.

PubMed
Microbial genomes: dealing with diversity.
Microbial genomes: dealing with diversity.
Curr Opin Microbiol. 2001 Jun ;4(3):285-9.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: