MotifScorer: using a compendium of microarrays to identify regulatory motifs.

Abstract

We describe MotifScorer, a program for systematic genome-wide identification of transcription sites. The program uses a compendium of gene expression microarrays and implements state-of-art partial least squares (PLSs) based regression and stepwise regression procedures. Candidate motifs from the upstream sequences of groups of co-regulated genes are identified and assigned a score using genomic background models and available motif finding tools. The use of a large library of expression data allows statistical comparative analysis of the specificity of motifs identified in different conditions. MotifScorer, which is written in Java and Matlab, manual and example files are available from the authors.