Epimetheus - a multi-profile normalizer for epigenomic sequencing data

BMC Bioinformatics
Mohamed-Ashick M SaleemHinrich Gronemeyer

Abstract

Exponentially increasing numbers of NGS-based epigenomic datasets in public repositories like GEO constitute an enormous source of information that is invaluable for integrative and comparative studies of gene regulatory mechanisms. One of today's challenges for such studies is to identify functionally informative local and global patterns of chromatin states in order to describe the regulatory impact of the epigenome in normal cell physiology and in case of pathological aberrations. Critically, the most preferred Chromatin ImmunoPrecipitation-Sequencing (ChIP-Seq) is inherently prone to significant variability between assays, which poses significant challenge on comparative studies. One challenge concerns data normalization to adjust sequencing depth variation. Currently existing tools either apply linear scaling corrections and/or are restricted to specific genomic regions, which can be prone to biases. To overcome these restrictions without any external biases, we developed Epimetheus, a genome-wide quantile-based multi-profile normalization tool for histone modification data and related datasets. Epimetheus has been successfully used to normalize epigenomics data in previous studies on X inactivation in breast cancer and in...Continue Reading

References

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Citations

Apr 20, 2018·Nucleic Acids Research·Michael J GuertinAndrew N Holding

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Datasets Mentioned

BETA
GM12878
GSM646365
GSM788366
GSM768313

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
PCR
ChIP
FAIRE-seq
in

Software Mentioned

LOESS
QC Generator
norm
NGS
Polyphemus
ChIPnorm
Epimetheus
DESeq
ChromHMM
ChIP

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