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chroGPS, a global chromatin positioning system for the functional analysis and visualization of the epigenome

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Font-Burgada, Joan, Reina, Oscar, Rossell, David and Azorin, Fernando (2013) chroGPS, a global chromatin positioning system for the functional analysis and visualization of the epigenome. Nucleic Acids Research, Volume 42 (Number 4). pp. 2126-2137. doi:10.1093/nar/gkt1186

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Official URL: http://dx.doi.org/10.1093/nar/gkt1186

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Abstract

Development of tools to jointly visualize the genome and the epigenome remains a challenge. chroGPS is a computational approach that addresses this question. chroGPS uses multidimensional scaling techniques to represent similarity between epigenetic factors, or between genetic elements on the basis of their epigenetic state, in 2D/3D reference maps. We emphasize biological interpretability, statistical robustness, integration of genetic and epigenetic data from heterogeneous sources, and computational feasibility. Although chroGPS is a general methodology to create reference maps and study the epigenetic state of any class of genetic element or genomic region, we focus on two specific kinds of maps: chroGPSfactors, which visualizes functional similarities between epigenetic factors, and chroGPSgenes, which describes the epigenetic state of genes and integrates gene expression and other functional data. We use data from the modENCODE project on the genomic distribution of a large collection of epigenetic factors in Drosophila, a model system extensively used to study genome organization and function. Our results show that the maps allow straightforward visualization of relationships between factors and elements, capturing relevant information about their functional properties that helps to interpret epigenetic information in a functional context and derive testable hypotheses.

Item Type: Journal Article
Subjects: Q Science > QH Natural history > QH301 Biology
Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science > Statistics
Library of Congress Subject Headings (LCSH): Chromatin, Genomics , Imaging systems
Journal or Publication Title: Nucleic Acids Research
Publisher: Oxford University Press
ISSN: 0305-1048
Official Date: November 2013
Dates:
DateEvent
November 2013Published
Volume: Volume 42
Number: Number 4
Page Range: pp. 2126-2137
DOI: 10.1093/nar/gkt1186
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
Funder: Spain. Ministerio de Economia y Competitividad’ (MEC), Generalitat de Catalunya (GC)
Grant number: CSD2006-49, BFU2009-07111, BFU2012-30724, BFU2012-30724 (MEC) ; SGR2009-1023 (GC)

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