Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism.

ABSTRACT: Characterization of cell type specific regulatory networks and elements is a major challenge in genomics, and emerging strategies frequently employ high-throughput genome-wide assays of transcription factor (TF) to DNA binding, histone modifications or chromatin state. However, these experiments remain too difficult/expensive for many laboratories to apply comprehensively to their system of interest. Here, we explore the potential of elucidating regulatory systems in varied cell types using computational techniques that rely on only data of gene expression, low-resolution chromatin accessibility, and TF-DNA binding specificities ('motifs'). We show that static computational motif scans overlaid with chromatin accessibility data reasonably approximate experimentally measured TF-DNA binding.

SUBMITTER: Blatti C 

PROVIDER: S-EPMC4417154 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature