A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription.

ABSTRACT:

Background

Multiple transcription factors (TFs) are involved in the generation of gene expression patterns, such as tissue-specific gene expression and pleiotropic immune responses. However, how combinations of TFs orchestrate diverse gene expression patterns is poorly understood. Here we propose a new measure for regulatory motif co-occurrence and a new methodology to systematically identify TF pairs significantly co-occurring in a set of promoter sequences.

Results

Initial analyses suggest that non-CpG promoters have a higher potential for combinatorial regulation than CpG island-associated promoters, and that co-occurrences are strongly influenced by motif similarity. We applied our method to large-scale gene expression data from various tissues, and showed how our measur

SUBMITTER: Vandenbon A 

PROVIDER: S-EPMC3521209 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature