GATHER: a systems approach to interpreting genomic signatures.
BACKGROUND
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.


BACKGROUND
GATHER is available at http://gather.genome.duke.edu/
Chang
Jeffrey T
JT
Department of Molecular Genetics and Microbiology, Duke Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, NC 27710, USA.
Nevins
Joseph R
JR
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D016172:DNA Fingerprinting / Q000379:methods*; D040641:Quantitative Trait Loci / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D049490:Systems Biology / Q000379:methods; D013598:Systems Theory