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Bioinformatics Advance Access published online on September 25, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl483
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 15, 2006
Revised August 23, 2006
Accepted September 11, 2006

Article

GATHER: a systems approach to interpreting genomic signatures

Jeffrey T. Chang 1 and Joseph R. Nevins 1 *

1 Duke Institute for Genome Sciences and Policy, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710

* To whom correspondence should be addressed.
Joseph R. Nevins, E-mail: j.nevins{at}duke.edu


  Abstract

Motivation: Understanding the full meaning of the biology captured in molecular profiles, within the context of the entire biological system, cannot be achieved with a simple examination of the individual genes in the signature. To facilitate such an understanding, we have developed GATHER, a tool that integrates various forms of available data to elucidate biological context within molecular signatures produced from high-throughput post-genomic assays.

Results: Analyzing the Rb/E2F tumor suppressor pathway, we show that GATHER identifies critical features of the pathway. We further show that GATHER identifies common biology in a series of otherwise unrelated gene expression signatures that each predict breast cancer outcome. We quantify the performance of GATHER and find that it successfully predicts 90% of the functions over a broad range of gene groups. We believe that GATHER provides an essential tool for extracting the full value from molecular signatures generated from genome-scale analyses.

Availability: GATHER is available at http://gather.genome.duke.edu/.

Associate Editor: Jonathan Wren
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