TargetOrtho: a phylogenetic footprinting tool to identify transcription factor targets.

ABSTRACT: The identification of the regulatory targets of transcription factors is central to our understanding of how transcription factors fulfill their many key roles in development and homeostasis. DNA-binding sites have been uncovered for many transcription factors through a number of experimental approaches, but it has proven difficult to use this binding site information to reliably predict transcription factor target genes in genomic sequence space. Using the nematode Caenorhabditis elegans and other related nematode species as a starting point, we describe here a bioinformatic pipeline that identifies potential transcription factor target genes from genomic sequences. Among the key features of this pipeline is the use of sequence conservation of transcription-factor-binding sites in related

SUBMITTER: Glenwinkel L 

PROVIDER: S-EPMC4012501 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature