Stability selection for regression-based models of transcription factor-DNA binding specificity.

ABSTRACT:

Motivation

The DNA binding specificity of a transcription factor (TF) is typically represented using a position weight matrix model, which implicitly assumes that individual bases in a TF binding site contribute independently to the binding affinity, an assumption that does not always hold. For this reason, more complex models of binding specificity have been developed. However, these models have their own caveats: they typically have a large number of parameters, which makes them hard to learn and interpret.

Results

We propose novel regression-based models of TF-DNA binding specificity, trained using high resolution in vitro data from custom protein-binding microarray (PBM) experiments. Our PBMs are specifically designed to cover a large number of putative DNA binding sites

SUBMITTER: Mordelet F 

PROVIDER: S-EPMC3694650 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature