Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.

ABSTRACT:

Background

cis-Regulatory modules (CRMs) of eukaryotic genes often contain multiple binding sites for transcription factors. The phenomenon that binding sites form clusters in CRMs is exploited in many algorithms to locate CRMs in a genome. This gives rise to the problem of calculating the statistical significance of the event that multiple sites, recognized by different factors, would be found simultaneously in a text of a fixed length. The main difficulty comes from overlapping occurrences of motifs. So far, no tools have been developed allowing the computation of p-values for simultaneous occurrences of different motifs which can overlap.

Results

We developed and implemented an algorithm computing the p-value that s different motifs occur respectively k1, ..., ks or more

SUBMITTER: Boeva V 

PROVIDER: S-EPMC2174486 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature