title: 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.
authors.affiliation: Department of Computer Sciences, University of Wisconsin, Madison, 53717, WI, USA.
authors.forename: Alireza
authors.initials: A
authors.lastname: Fotuhi Siahpirani
authors.affiliation: La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, 92037, CA, USA.
authors.forename: Ferhat
authors.initials: F
authors.lastname: Ay
authors.affiliation: Wisconsin Institute for Discovery, University of Wisconsin, Madison, 53717, WI, USA. sroy@biostat.wisc.edu.|Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, 53717, WI, USA. sroy@biostat.wisc.edu.
authors.forename: Sushmita
authors.initials: S
authors.lastname: Roy
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics*; D016000:Cluster Analysis; D016678:Genome; D006801:Humans; D007621:Karyotyping / Q000379:methods*; D051379:Mice; D008968:Molecular Conformation
chemical_list: D002843:Chromatin