A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks.

ABSTRACT:

Background

Deciphering cis-regulatory networks has become an attractive yet challenging task. This paper presents a simple method for cis-regulatory network discovery which aims to avoid some of the common problems of previous approaches.

Results

Using promoter sequences and gene expression profiles as input, rather than clustering the genes by the expression data, our method utilizes co-expression neighborhood information for each individual gene, thereby overcoming the disadvantages of current clustering based models which may miss specific information for individual genes. In addition, rather than using a motif database as an input, it implements a simple motif count table for each enumerated k-mer for each gene promoter sequence. Thus, it can be used for species where pr

SUBMITTER: Gao Z 

PROVIDER: S-EPMC3549801 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature