Transcription factor binding sites prediction based on modified nucleosomes.

ABSTRACT: In computational methods, position weight matrices (PWMs) are commonly applied for transcription factor binding site (TFBS) prediction. Although these matrices are more accurate than simple consensus sequences to predict actual binding sites, they usually produce a large number of false positive (FP) predictions and so are impoverished sources of information. Several studies have employed additional sources of information such as sequence conservation or the vicinity to transcription start sites to distinguish true binding regions from random ones. Recently, the spatial distribution of modified nucleosomes has been shown to be associated with different promoter architectures. These aligned patterns can facilitate DNA accessibility for transcription factors. We hypothesize that using data f

SUBMITTER: Talebzadeh M 

PROVIDER: S-EPMC3931712 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature