Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data.

ABSTRACT:

Motivation

Unraveling the transcriptional regulatory program mediated by transcription factors (TFs) is a fundamental objective of computational biology, yet still remains a challenge.

Method

Here, we present a new methodology that integrates microarray and TF binding data for unraveling transcriptional regulatory networks. The algorithm is based on a two-stage constrained matrix decomposition model. The model takes into account the non-linear structure in gene expression data, particularly in the TF-target gene interactions and the combinatorial nature of gene regulation by TFs. The gene expression profile is modeled as a linear weighted combination of the activity profiles of a set of TFs. The TF activity profiles are deduced from the expression levels of TF target genes,

SUBMITTER: Li H 

PROVIDER: S-EPMC2519161 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature