Submitted on November 22, 2006
Accepted on October 8, 2007
PADGE: analysis of heterogeneous patterns of differential gene expression
Li Li1, Amitabha Chaudhuri2, John Chant3, and Zhijun Tang1*
1 Bioinformatics, Genentech Inc., South San Francisco, California, United States
2 Molecular Oncology, Genentech Inc., South San Francisco, California, United States
3 Molecular Biology, Genentech Inc., South San Francisco, California, United States
* To whom correspondence should be addressed. E-mail: jtang{at}gene.com.
We have devised a novel analysis approach, Percentile Analysis for Differential Gene Expression (PADGE) for identifying genes differentially expressed between two groups of heterogeneous samples. PADGE was designed to compare expression profiles of sample subgroups at a series of percentile cutoffs and to examine the trend of relative expression between sample groups as expression level increases. Simulation studies showed that PADGE has more statistical power than t statistics, COPA (Tomlins, et al, 2005) and Kurtosis (Teschendorff, et al, 2006). Application of PADGE to microarray datasets in tumor tissues demonstrated its utility in prioritizing cancer genes encoding potential therapeutic targets or diagnostic markers. A web application was developed for researchers to analyze large gene expression dataset from heterogeneous biological samples and identify differentially expressed genes between subsets of sample classes using PADGE and other available approaches.
