IASeq: integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets.

ABSTRACT:

Background

ChIP-seq provides new opportunities to study allele-specific protein-DNA binding (ASB). However, detecting allelic imbalance from a single ChIP-seq dataset often has low statistical power since only sequence reads mapped to heterozygote SNPs are informative for discriminating two alleles.

Results

We develop a new method iASeq to address this issue by jointly analyzing multiple ChIP-seq datasets. iASeq uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins. Using the discovered correlation patterns, the model allows one to borrow information across datasets to improve detection of allelic imbalance. Application of iASeq to 77 ChIP-seq samples from 40 ENCODE datasets and 1 genomic DNA sample in GM12878

SUBMITTER: Wei Y 

PROVIDER: S-EPMC3576346 | biostudies-literature | 2012 Nov

REPOSITORIES: biostudies-literature