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EpiChIP : gene-by-gene quantification of epigenetic modification levels
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Hebenstreit, Daniel, Gu, M., Haider, S., Turner, D. J., Lio, P. and Teichmann, Sarah A. (2011) EpiChIP : gene-by-gene quantification of epigenetic modification levels. Nucleic Acids Research, Vol. 39 (No. 5). e27-e27. doi:10.1093/nar/gkq1226 ISSN 0305-1048.
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Official URL: http://dx.doi.org/10.1093/nar/gkq1226
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 H3K9/14ac histone modification in Th cells and an accompanying IgG control, we present an analysis strategy that alternates between single gene and global data distribution levels and allows a clear distinction between experimental background and signal. Curve fitting permits false discovery rate-based classification of genes as modified versus unmodified. We have developed a software package called EpiChIP that carries out this type of analysis, including integration with and visualization of gene expression data.
Item Type: | Journal Article | ||||
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||
Journal or Publication Title: | Nucleic Acids Research | ||||
Publisher: | Oxford University Press | ||||
ISSN: | 0305-1048 | ||||
Official Date: | 2011 | ||||
Dates: |
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Volume: | Vol. 39 | ||||
Number: | No. 5 | ||||
Page Range: | e27-e27 | ||||
DOI: | 10.1093/nar/gkq1226 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Restricted or Subscription Access |
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