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Bioinformatics Advance Access originally published online on September 25, 2006
Bioinformatics 2006 22(23):2926-2933; 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

GATHER: a systems approach to interpreting genomic signatures

Jeffrey T. Chang and Joseph R. Nevins *

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

*To whom correspondence should be addressed.

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/

Contact: j.nevins{at}duke.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on July 15, 2006; revised on August 23, 2006; accepted on September 11, 2006

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