Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites.

ABSTRACT:

Background

The identifying of binding sites for transcription factors is a key component of gene regulatory network analysis. This is often done using position-weight matrices (PWMs). Because of the importance of in silico mapping of tentative binding sites, we previously developed an approach for PWM optimization that substantially improves the accuracy of such mapping.

Results

The present work implements the optimization algorithm applied to the existing PWM for GATA-3 transcription factor and builds a new di-nucleotide PWM. The existing available PWM is based on experimental data adopted from Jaspar. The optimized PWM substantially improves the sensitivity and specificity of the TF mapping compared to the conventional applications. The refined PWM also facilitates in sili

SUBMITTER: Nandi S 

PROVIDER: S-EPMC3481455 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature