A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.

ABSTRACT:

Motivation

The position-weight matrix (PWM) is a useful representation of a transcription factor binding site (TFBS) sequence pattern because the PWM can be estimated from a small number of representative TFBS sequences. However, because the PWM probability model assumes independence between individual nucleotide positions, the PWMs for some TFs poorly discriminate binding sites from non-binding-sites that have similar sequence content. Since the local three-dimensional DNA structure ('shape') is a determinant of TF binding specificity and since DNA shape has a significant sequence-dependence, we combined DNA shape-derived features into a TF-generalized regulatory score and tested whether the score could improve PWM-based discrimination of TFBS from non-binding-sites.

Results

SUBMITTER: Yang J 

PROVIDER: S-EPMC4838056 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature