DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks

Functional genomic and epigenomic research relies fundamentally on sequencing based methods like ChIP-seq for the detection of DNA-protein interactions. These techniques return large, high dimensional data sets with visually complex structures, such as multi-modal peaks extended over large genomic r...

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Bibliographic Details
Published in:BMC bioinformatics 2016-12, Vol.17 (Suppl 16), p.447-447, Article 447
Main Authors: Lukauskas, Saulius, Visintainer, Roberto, Sanguinetti, Guido, Schweikert, Gabriele B
Format: Article
Language:English
Subjects:
Chromatin Immunoprecipitation
Cluster Analysis
Computer Simulation
DNA - metabolism
DNA sequencing
DNA-Binding Proteins - metabolism
Epigenesis, Genetic
Epigenetic inheritance
Epigenomics - methods
Genome, Human
Histone Code
Humans
Leukemia - genetics
Methods
Observations
Protein-protein interactions
Software
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Summary:Functional genomic and epigenomic research relies fundamentally on sequencing based methods like ChIP-seq for the detection of DNA-protein interactions. These techniques return large, high dimensional data sets with visually complex structures, such as multi-modal peaks extended over large genomic regions. Current tools for visualisation and data exploration represent and leverage these complex features only to a limited extent. We present DGW, an open source software package for simultaneous alignment and clustering of multiple epigenomic marks. DGW uses Dynamic Time Warping to adaptively rescale and align genomic distances which allows to group regions of interest with similar shapes, thereby capturing the structure of epigenomic marks. We demonstrate the effectiveness of the approach in a simulation study and on a real epigenomic data set from the ENCODE project. Our results show that DGW automatically recognises and aligns important genomic features such as transcription start sites and splicing sites from histone marks. DGW is available as an open source Python package.
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-016-1306-0