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Detecting cis-regulatory modules by modeling correlated structures in genomic sequences (2006).
| Content Provider | CiteSeerX |
|---|---|
| Author | Zhou, Qing |
| Abstract | Gene transcription is regulated by interactions between transcription factors (TFs) and their DNA binding sites. The common binding pattern of one TF is called a mo-tif. The regulatory information for a eukaryotic gene is encoded in cis-regulatory modules (CRMs) composed of binding sites of multiple TFs. I propose a hierarchical mixture approach to model the cis-regulatory module structure by considering the co-localization of multiple transcription factor binding sites (TFBS’s) to the same module. Based on the model, a de novo motif-module discovery algorithm, CisMod-ule, is developed for Bayesian inference about module locations and within-module motif sites. I have applied this approach to the characterization and discovery of novel CRMs that drive gene expression in muscle development in Ciona savignyi. Furthermore, evolutionary constraints among TFBS’s in related species provide an independent piece of information for the identification of motifs. To combine in de novo motif discovery the two pieces of information contained in module structure and cross-species orthology, I develop a coupled hidden Markov model (c-HMM) where |
| File Format | |
| Publisher Date | 2006-01-01 |
| Access Restriction | Open |
| Subject Keyword | Dna Binding Site Multiple Transcription Factor Multiple Tfs Genomic Sequence Module Structure Regulatory Information Coupled Hidden Markov Model Cross-species Orthology Muscle Development Ciona Savignyi Cis-regulatory Module Structure Transcription Factor Module Location Gene Transcription Evolutionary Constraint Novel Crms Gene Expression Within-module Motif Site Cis-regulatory Module Motif-module Discovery Algorithm Bayesian Inference Hierarchical Mixture Approach Eukaryotic Gene Independent Piece Common Binding Pattern Related Specie Correlated Structure |
| Content Type | Text |
