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BMC Bioinformatics. 2017 May 12;18(1):259. doi: 10.1186/s12859-017-1655-3.

Epimetheus - a multi-profile normalizer for epigenomic sequencing data.

Author information

1
Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.
2
Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France. marco@igbmc.u-strasbg.fr.
3
Centre National de la Recherche Scientifique UMR 7104, Illkirch, France. marco@igbmc.u-strasbg.fr.
4
Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France. marco@igbmc.u-strasbg.fr.
5
Université de Strasbourg, Illkirch, France. marco@igbmc.u-strasbg.fr.
6
Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France. hg@igbmc.u-strasbg.fr.
7
Centre National de la Recherche Scientifique UMR 7104, Illkirch, France. hg@igbmc.u-strasbg.fr.
8
Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France. hg@igbmc.u-strasbg.fr.
9
Université de Strasbourg, Illkirch, France. hg@igbmc.u-strasbg.fr.

Abstract

BACKGROUND:

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.

RESULTS:

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.

CONCLUSIONS:

Epimetheus has been successfully used to normalize epigenomics data in previous studies on X inactivation in breast cancer and in integrative studies of neuronal cell fate acquisition and tumorigenic transformation; Epimetheus is freely available to the scientific community.

KEYWORDS:

ChIP-seq; Epigenome; Multi-sample analysis; Quantile-based data normalization

PMID:
28499349
PMCID:
PMC5429578
DOI:
10.1186/s12859-017-1655-3
[Indexed for MEDLINE]
Free PMC Article

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