De-novo discovery of differentially abundant transcription factor binding sites including their positional preference.

ABSTRACT: Transcription factors are a main component of gene regulation as they activate or repress gene expression by binding to specific binding sites in promoters. The de-novo discovery of transcription factor binding sites in target regions obtained by wet-lab experiments is a challenging problem in computational biology, which has not been fully solved yet. Here, we present a de-novo motif discovery tool called Dispom for finding differentially abundant transcription factor binding sites that models existing positional preferences of binding sites and adjusts the length of the motif in the learning process. Evaluating Dispom, we find that its prediction performance is superior to existing tools for de-novo motif discovery for 18 benchmark data sets with planted binding sites, and for a metazoan

SUBMITTER: Keilwagen J 

PROVIDER: S-EPMC3037384 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature