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

ABSTRACT: 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.

SUBMITTER: Fotuhi Siahpirani A

PROVIDER: S-EPMC4882777 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature

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

Fotuhi Siahpirani Alireza A Ay Ferhat F Roy Sushmita S

Genome biology 20160527 1

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 c ...[more]

PMID: 27233632

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