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CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting

Henry R Bigelow, Adam S Wenick, Allan Wong and Oliver Hobert*

Author Affiliations

Department of Biochemistry and Molecular Biophysics, Columbia University, College of Physicians and Surgeons, 701 West 168th Street, New York, NY 10032, USA

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BMC Bioinformatics 2004, 5:27  doi:10.1186/1471-2105-5-27

Published: 12 March 2004

Abstract

Background

All known genomes code for a large number of transcription factors. It is important to develop methods that will reveal how these transcription factors act on a genome wide level, that is, through what target genes they exert their function.

Results

We describe here a program pipeline aimed at identifying transcription factor target genes in whole genomes. Starting from a consensus binding site, represented as a weight matrix, potential sites in a pre-filtered genome are identified and then further filtered by assessing conservation of the putative site in the genome of a related species, a process called phylogenetic footprinting. CisOrtho has been successfully used to identify targets for two homeodomain transcription factors in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae.

Conclusions

CisOrtho will identify targets of other nematode transcription factors whose DNA binding specificity is known and can be easily adapted to search other genomes for transcription factor targets.