Transcriptional programs: modelling higher order structure in transcriptional control.

ABSTRACT:

Background

Transcriptional regulation is an important part of regulatory control in eukaryotes. Even if binding motifs for transcription factors are known, the task of finding binding sites by scanning sequences is plagued by false positives. One way to improve the detection of binding sites from motifs is by taking cooperativity of transcription factor binding into account. We propose a non-parametric probabilistic model, similar to a document topic model, for detecting transcriptional programs, groups of cooperative transcription factors and co-regulated genes. The analysis results in transcriptional programs which generalise both transcriptional modules and TF-target gene incidence matrices and provide a higher-level summary of these structures. The method is independent of prio

SUBMITTER: Reid JE 

PROVIDER: S-EPMC2725141 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature