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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 ISSN 0305-1048.
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WRAP_Nucl. Acids Res.-2013-Font-Burgada-nar-gkt1186.pdf - Published Version Available under License Creative Commons Attribution Non-commercial. Download (1874Kb) | Preview |
Official URL: http://dx.doi.org/10.1093/nar/gkt1186
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 | ||||
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| Subjects: | Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics |
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| Divisions: | Faculty of Science, Engineering and Medicine > 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: |
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| 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 (Creative Commons) | ||||
| Date of first compliant deposit: | 26 December 2015 | ||||
| Date of first compliant Open Access: | 26 December 2015 | ||||
| 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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