Paper Info
Title
A statistical method for finding transcription factor binding sites.
Abstract
Understanding the mechanisms that determine the regulation of gene expression is an important and challenging problem. A fundamental subproblem is to identify DNA-binding sites for unknown regulatory factors, given a collection of genes believed to be coregulated, and given the noncoding DNA sequences near those genes. We present an enumerative statistical method for identifying good candidates for such transcription factor binding sites. Unlike local search techniques such as Expectation Maximization and Gibbs samplers that may not reach a global optimum, the method proposed here is guaranteed to produce the motifs with greatest z-scores. We discuss the results of experiments in which this algorithm was used to locate candidate binding sites in several well studied pathways of S. cerevisiae, as well as gene clusters from some of the hybridization microarray experiments.
Year
Venue
Keywords
2000
ISMB
statistical method,finding transcription factor,transcription factor binding site,local search,transcription factor,gene expression
Field
DocType
Volume
Gene,Binding site,Noncoding DNA,DNA binding site,Biology,Regulation of gene expression,Response element,Local search (optimization),Bioinformatics,TRANSFAC
Conference
8
ISSN
ISBN
Citations 
1553-0833
1-57735-115-0
86
PageRank 
References 
Authors
15.40
14
2
Name
Order
Citations
PageRank
Saurabh Sinha152948.96
Martin Tompa21103149.69