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BMCBI
2004

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

13 years 5 months ago
CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting
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...
Henry R. Bigelow, Adam S. Wenick, Allan Wong, Oliv
Added 16 Dec 2010
Updated 16 Dec 2010
Type Journal
Year 2004
Where BMCBI
Authors Henry R. Bigelow, Adam S. Wenick, Allan Wong, Oliver Hobert
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