Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways.

ABSTRACT: Understanding of gene regulatory networks requires discovery of expression modules within gene co-expression networks and identification of promoter motifs and corresponding transcription factors that regulate their expression. A commonly used method for this purpose is a top-down approach based on clustering the network into a range of densely connected segments, treating these segments as expression modules, and extracting promoter motifs from these modules. Here, we describe a novel bottom-up approach to identify gene expression modules driven by known cis-regulatory motifs in the gene promoters. For a specific motif, genes in the co-expression network are ranked according to their probability of belonging to an expression module regulated by that motif. The ranking is conducted via mot

SUBMITTER: Ma S 

PROVIDER: S-EPMC3789834 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature