A simple hyper-geometric approach for discovering putative transcription factor binding sites

Yoseph Barash, Gill Bejerano, Nir Friedman

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

51 Scopus citations

Abstract

A central issue in molecular biology is understanding the regulatory mechanisms that control gene expression. The recent flood of genomic and postgenomic data opens the way for computational methods elucidating the key components that play a role in these mechanisms. One important consequence is the ability to recognize groups of genes that are co-expressed using microarray expression data. We then wish to identify in-silico putative transcription factor binding sites in the promoter regions of these gene, that might explain the coregulation, and hint at possible regulators. In this paper we describe a simple and fast, yet powerful, two stages approach to this task. Using a rigorous hypergeometric statistical analysis and a straightforward computational procedure we find small conserved sequence kernels. These are then stochastically expanded into PSSMs using an EM-like procedure. We demonstrate the utility and speed of our methods by applying them to several data sets from recent literature. We also compare these results with those of MEME when run on the same sets.

Original languageAmerican English
Title of host publicationAlgorithms in Bioinformatics - First International Workshop, WABI 2001 Århus Denmark, August 28-31, 2001 Proceedings
EditorsBernard M. E. Moret, Olivier Gascuel
PublisherSpringer Verlag
Pages278-293
Number of pages16
ISBN (Print)3540425160
DOIs
StatePublished - 2001
Event1st International Workshop on Algorithms in Bioinformatics, WABI 2001 - Arhus, Denmark
Duration: 28 Aug 200131 Aug 2001

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume2149
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference1st International Workshop on Algorithms in Bioinformatics, WABI 2001
Country/TerritoryDenmark
CityArhus
Period28/08/0131/08/01

Bibliographical note

Publisher Copyright:
© Springer-Verlag Berlin Heidelberg 2001.

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