A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Fotuhi Siahpirani, Alireza; Ay, Ferhat; Roy, Sushmita
• Is Part Of: Genome biology. Volume 17:Issue 1(2016)
• Page Start: 1
• Page End: 18
• Publication Date: 2016-12
• Subjects: Genomes -- Periodicals; Biology -- Periodicals; Molecular biology -- Periodicals; 572.8633
• DOI: 10.1186/s13059-016-0962-8
• Languages: English
• ISSNs: 1474-760X

Abstract

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.