Subtypes of associated protein-DNA (Transcription Factor-Transcription Factor Binding Site) patterns.

ABSTRACT: In protein-DNA interactions, particularly transcription factor (TF) and transcription factor binding site (TFBS) bindings, associated residue variations form patterns denoted as subtypes. Subtypes may lead to changed binding preferences, distinguish conserved from flexible binding residues and reveal novel binding mechanisms. However, subtypes must be studied in the context of core bindings. While solving 3D structures would require huge experimental efforts, recent sequence-based associated TF-TFBS pattern discovery has shown to be promising, upon which a large-scale subtype study is possible and desirable. In this article, we investigate residue-varying subtypes based on associated TF-TFBS patterns. By re-categorizing the patterns with respect to varying TF amino acids, statistically sig

SUBMITTER: Chan TM 

PROVIDER: S-EPMC3479201 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature