EpiChIP: gene-by-gene quantification of epigenetic modification levels.

ABSTRACT: The combination of chromatin immunoprecipitation with next-generation sequencing technology (ChIP-seq) is a powerful and increasingly popular method for mapping protein-DNA interactions in a genome-wide fashion. The conventional way of analyzing this data is to identify sequencing peaks along the chromosomes that are significantly higher than the read background. For histone modifications and other epigenetic marks, it is often preferable to find a characteristic region of enrichment in sequencing reads relative to gene annotations. For instance, many histone modifications are typically enriched around transcription start sites. Calculating the optimal window that describes this enrichment allows one to quantify modification levels for each individual gene. Using data sets for the H3K9/14a

SUBMITTER: Hebenstreit D 

PROVIDER: S-EPMC3061070 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature