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A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions

Chromosome conformation capture methods are being increasingly used to study three-dimensional genome architecture in multiple cell types and species. An important challenge is to examine changes in three-dimensional architecture across cell types and species. We present Arboretum-Hi-C, a multi-task...

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Detalles Bibliográficos
Autores principales: Fotuhi Siahpirani, Alireza, Ay, Ferhat, Roy, Sushmita
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4882777/
https://www.ncbi.nlm.nih.gov/pubmed/27233632
http://dx.doi.org/10.1186/s13059-016-0962-8
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author Fotuhi Siahpirani, Alireza
Ay, Ferhat
Roy, Sushmita
author_facet Fotuhi Siahpirani, Alireza
Ay, Ferhat
Roy, Sushmita
author_sort Fotuhi Siahpirani, Alireza
collection PubMed
description Chromosome conformation capture methods are being increasingly used to study three-dimensional genome architecture in multiple cell types and species. An important challenge is to examine changes in three-dimensional architecture across cell types and species. We present Arboretum-Hi-C, a multi-task spectral clustering method, to identify common and context-specific aspects of genome architecture. Compared to standard clustering, Arboretum-Hi-C produced more biologically consistent patterns of conservation. Most clusters are conserved and enriched for either high- or low-activity genomic signals. Most genomic regions diverge between clusters with similar chromatin state except for a few that are associated with lamina-associated domains and open chromatin. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-0962-8) contains supplementary material, which is available to authorized users.
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spelling pubmed-48827772016-05-28 A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions Fotuhi Siahpirani, Alireza Ay, Ferhat Roy, Sushmita Genome Biol Method Chromosome conformation capture methods are being increasingly used to study three-dimensional genome architecture in multiple cell types and species. An important challenge is to examine changes in three-dimensional architecture across cell types and species. We present Arboretum-Hi-C, a multi-task spectral clustering method, to identify common and context-specific aspects of genome architecture. Compared to standard clustering, Arboretum-Hi-C produced more biologically consistent patterns of conservation. Most clusters are conserved and enriched for either high- or low-activity genomic signals. Most genomic regions diverge between clusters with similar chromatin state except for a few that are associated with lamina-associated domains and open chromatin. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-0962-8) contains supplementary material, which is available to authorized users. BioMed Central 2016-05-27 /pmc/articles/PMC4882777/ /pubmed/27233632 http://dx.doi.org/10.1186/s13059-016-0962-8 Text en © Fotuhi Siahpirani et al. 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Fotuhi Siahpirani, Alireza
Ay, Ferhat
Roy, Sushmita
A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions
title A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions
title_full A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions
title_fullStr A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions
title_full_unstemmed A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions
title_short A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions
title_sort multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4882777/
https://www.ncbi.nlm.nih.gov/pubmed/27233632
http://dx.doi.org/10.1186/s13059-016-0962-8
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