JAMIE: joint analysis of multiple ChIP-chip experiments.

ABSTRACT:

Motivation

Chromatin immunoprecipitation followed by genome tiling array hybridization (ChIP-chip) is a powerful approach to identify transcription factor binding sites (TFBSs) in target genomes. When multiple related ChIP-chip datasets are available, analyzing them jointly allows one to borrow information across datasets to improve peak detection. This is particularly useful for analyzing noisy datasets.

Results

We propose a hierarchical mixture model and develop an R package JAMIE to perform the joint analysis. The genome is assumed to consist of background and potential binding regions (PBRs). PBRs have context-dependent probabilities to become bona fide binding sites in individual datasets. This model captures the correlation among datasets, which provides basis for shar

SUBMITTER: Wu H 

PROVIDER: S-EPMC2905557 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature