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

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/.

Fig. 1

Simplified UML diagram of the architecture of GO::TermFinder and associated modules. Public methods defined by the abstract base class, GO::OntologyProvider, which are implemented by concrete subclasses, such as the GO::OntologyProvider::OntologyParser class that we have written, return either a single GO::Node, or an array of GO::Node instances. A subset of the public interface to GO::Node is shown, illustrating the various methods that exist to query the attributes of a GO::Node, as well as to traverse the GO structure.

Fig. 2

Visualizing output from GO::TermFinder. GO graph layout that includes the significant GO nodes annotated by the ‘methioine cluster’, which contains ICY2, MET11, MXR1, SAM3, MET28, STR3, MMP1, MET1, SER33, MHT1, MET14, MET16, MET3, MET10, ECM17, MET2, MUP1 and MET6. The color of the nodes is an indication of their Bonferroni corrected P-value (orange <= 1e-10; yellow 1e-10 to 1e-8; green 1e-8 to 1e-6; cyan 1e-6 to 1e-4; blue 1e-4 to 1e-2; tan > 0.01).