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

Bigelow, Henry; Wenick, Adam; Wong, Allan; Hobert, Oliver

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.

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Title
BMC Bioinformatics
DOI
https://doi.org/10.1186/1471-2105-5-27

More About This Work

Academic Units
Biological Sciences
Published Here
September 9, 2014
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