We found a match
Your institution may have rights to this item. Sign in to continue.
- Title
Genome-wide discovery of transcriptional modules from DNA sequence and gene expression.
- Authors
E. Segal; R. Yelensky; D. Koller
- Abstract
In this paper, we describe an approach for understanding transcriptional regulation from both gene expression and promoter sequence data. We aim to identify transcriptional modules--sets of genes that are co-regulated in a set of experiments, through a common motif profile. Using the EM algorithm, our approach refines both the module assignment and the motif profile so as to best explain the expression data as a function of transcriptional motifs. It also dynamically adds and deletes motifs, as required to provide a genome-wide explanation of the expression data. We evaluate the method on two Saccharomyces cerevisiae gene expression data sets, showing that our approach is better than a standard one at recovering known motifs and at generating biologically coherent modules. We also combine our results with binding localization data to obtain regulatory relationships with known transcription factors, and show that many of the inferred relationships have support in the literature. Contact: eran@cs.stanford.edu Keywords: probabilistic models, gene expression, transcriptional regulation.
- Subjects
GENE expression; PROBABILITY theory; SACCHAROMYCES cerevisiae; GENOMES
- Publication
Bioinformatics, 2009, Vol 19, p273
- ISSN
1367-4803
- Publication type
Article