JSM 2005 - Toronto

Abstract #303394

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Legend: = Applied Session, = Theme Session, = Presenter
Activity Number: 515
Type: Contributed
Date/Time: Thursday, August 11, 2005 : 10:30 AM to 12:20 PM
Sponsor: Biometrics Section
Abstract - #303394
Title: Computation-based Discovery of Cis-regulatory Modules by Hidden Markov Model
Author(s): Jing Wu*+
Companies: Purdue University
Address: 150 N University Street, West Lafayette, IN, 47907, United States
Keywords: hidden Markov model ; cis-regulatory module ; motif ; positional weight metrix ; transcription factor ; binding site
Abstract:

A key component in genome sequence analysis is the identification of regions of the genome that contain regulatory information. In higher eukaryotes, this information is organized into modular units called cis-regulatory modules. Each module contains multiple binding sites for a specific combination of several transcription factors. In this article, we propose a hidden Markov model to describe the cis-regulatory module structure. The hidden Markov model provides good stochastic machinery to generate sequences with modules and the inside motifs. Utilizing all available position weight matrices, we develop a new algorithm to identify the hidden path for modules and within-module motif sites. Our method is applied to real datasets with experimentally evaluated transcription factor binding sites. The method not only identifies motif clusters but enhances the predictive specificity for individual motifs. This is joint work with Dr. Jun Xie.

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Revised March 2005