Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding.

ABSTRACT:

Background

The combinatorial binding of trans-acting factors (TFs) to the DNA is critical to the spatial and temporal specificity of gene regulation. For certain regulatory regions, more than one regulatory module (set of TFs that bind together) are combined to achieve context-specific gene regulation. However, previous approaches are limited to either pairwise TF co-association analysis or assuming that only one module is used in each regulatory region.

Results

We present a new computational approach that models the modular organization of TF combinatorial binding. Our method learns compact and coherent regulatory modules from in vivo binding data using a topic model. We found that the binding of 115 TFs in K562 cells can be organized into 49 interpretable modules. Furtherm

SUBMITTER: Guo Y 

PROVIDER: S-EPMC5219757 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature