2004 Articles
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 genomes for transcription factor targets.
Files
-
1471-2105-5-27.pdf application/pdf 518 KB Download File
-
1471-2105-5-27.xml application/xml 51 KB Download File
Also Published In
- 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