CisMiner: genome-wide in-silico cis-regulatory module prediction by fuzzy itemset mining.

ABSTRACT: Eukaryotic gene control regions are known to be spread throughout non-coding DNA sequences which may appear distant from the gene promoter. Transcription factors are proteins that coordinately bind to these regions at transcription factor binding sites to regulate gene expression. Several tools allow to detect significant co-occurrences of closely located binding sites (cis-regulatory modules, CRMs). However, these tools present at least one of the following limitations: 1) scope limited to promoter or conserved regions of the genome; 2) do not allow to identify combinations involving more than two motifs; 3) require prior information about target motifs. In this work we present CisMiner, a novel methodology to detect putative CRMs by means of a fuzzy itemset mining approach able to operat

SUBMITTER: Navarro C 

PROVIDER: S-EPMC4182448 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature