Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data.

ABSTRACT:

Motivation

Chromatin immunoprecipitation (ChIP) experiments followed by array hybridization, or ChIP-chip, is a powerful approach for identifying transcription factor binding sites (TFBS) and has been widely used. Recently, massively parallel sequencing coupled with ChIP experiments (ChIP-seq) has been increasingly used as an alternative to ChIP-chip, offering cost-effective genome-wide coverage and resolution up to a single base pair. For many well-studied TFs, both ChIP-seq and ChIP-chip experiments have been applied and their data are publicly available. Previous analyses have revealed substantial technology-specific binding signals despite strong correlation between the two sets of results. Therefore, it is of interest to see whether the two data sources can be combined to enha

SUBMITTER: Choi H 

PROVIDER: S-EPMC2732365 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature