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2003
Springer

Modeling dependencies in protein-DNA binding sites

9 years 9 months ago
Modeling dependencies in protein-DNA binding sites
The availability of whole genome sequences and high-throughput genomic assays opens the door for in silico analysis of transcription regulation. This includes methods for discovering and characterizing the binding sites of DNA-binding proteins, such as transcription factors. A common representation of transcription factor binding sites is a position specific score matrix (PSSM). This representation makes the strong assumption that binding site positions are independent of each other. In this work, we explore Bayesian network representations of binding sites that provide different tradeoffs between complexity (number of parameters) and the richness of dependencies between positions. We develop the formal machinery for learning such models from data and for estimating the statistical significance of putative binding sites. We then evaluate the ramifications of these richer representations in characterizing binding site motifs and predicting their genomic locations. We show that these ri...
Yoseph Barash, Gal Elidan, Nir Friedman, Tommy Kap
Added 03 Dec 2009
Updated 03 Dec 2009
Type Conference
Year 2003
Where RECOMB
Authors Yoseph Barash, Gal Elidan, Nir Friedman, Tommy Kaplan
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