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Open Access Highly Accessed Software

GOLEM: an interactive graph-based gene-ontology navigation and analysis tool

Rachel SG Sealfon1, Matthew A Hibbs12, Curtis Huttenhower12, Chad L Myers12 and Olga G Troyanskaya12*

Author Affiliations

1 Department of Computer Science, Princeton University, 35 Olden Street, Princeton, NJ, USA

2 Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Labs, Princeton, NJ, USA

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BMC Bioinformatics 2006, 7:443  doi:10.1186/1471-2105-7-443

Published: 10 October 2006

Abstract

Background

The Gene Ontology has become an extremely useful tool for the analysis of genomic data and structuring of biological knowledge. Several excellent software tools for navigating the gene ontology have been developed. However, no existing system provides an interactively expandable graph-based view of the gene ontology hierarchy. Furthermore, most existing tools are web-based or require an Internet connection, will not load local annotations files, and provide either analysis or visualization functionality, but not both.

Results

To address the above limitations, we have developed GOLEM (Gene Ontology Local Exploration Map), a visualization and analysis tool for focused exploration of the gene ontology graph. GOLEM allows the user to dynamically expand and focus the local graph structure of the gene ontology hierarchy in the neighborhood of any chosen term. It also supports rapid analysis of an input list of genes to find enriched gene ontology terms. The GOLEM application permits the user either to utilize local gene ontology and annotations files in the absence of an Internet connection, or to access the most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global and organism-specific searches by gene ontology term name, gene ontology id and gene name.

Conclusion

GOLEM is a useful software tool for biologists interested in visualizing the local directed acyclic graph structure of the gene ontology hierarchy and searching for gene ontology terms enriched in genes of interest. It is freely available both as an application and as an applet at http://function.princeton.edu/GOLEM webcite.