GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes

Elizabeth I Boyle; Shuai Weng; Jeremy Gollub; Heng Jin; David Botstein; J Michael Cherry; Gavin Sherlock

doi:10.1093/bioinformatics/bth456

GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes

Bioinformatics. 2004 Dec 12;20(18):3710-5. doi: 10.1093/bioinformatics/bth456. Epub 2004 Aug 5.

Authors

Elizabeth I Boyle¹, Shuai Weng, Jeremy Gollub, Heng Jin, David Botstein, J Michael Cherry, Gavin Sherlock

Affiliation

¹ Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.

Abstract

Summary: GO::TermFinder comprises a set of object-oriented Perl modules for accessing Gene Ontology (GO) information and evaluating and visualizing the collective annotation of a list of genes to GO terms. It can be used to draw conclusions from microarray and other biological data, calculating the statistical significance of each annotation. GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script.

Availability: The full source code and documentation for GO::TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/.

Publication types

Research Support, U.S. Gov't, P.H.S.

MeSH terms

Abstracting and Indexing / methods
Database Management Systems*
Databases, Protein*
Gene Expression Profiling / methods*
Information Storage and Retrieval
Natural Language Processing*
Oligonucleotide Array Sequence Analysis / methods*
Programming Languages
Software*
User-Computer Interface*
Vocabulary, Controlled

Abstract

Publication types

MeSH terms

Grants and funding