Detecting community structures in Hi-C genomic data

Irineo Cabreros, Emmanuel Abbe, Aristotelis Tsirigos

Research output: Chapter in Book/Report/Conference proceedingConference contribution

14 Scopus citations

Abstract

Community detection (CD) algorithms are applied to Hi-C data to discover new communities of loci in the 3D conformation of human and mouse DNA. We find that CD has some distinct advantages over pre-existing methods: (1) it is capable of finding a variable number of communities, (2) it can detect communities of DNA loci either adjacent or distant in the 1D sequence, and (3) it allows us to obtain a principled value of k, the number of communities present. Forcing k = 2, our method recovers earlier findings of Lieberman-Aiden, et al. (2009), but letting k be a parameter, our method obtains as optimal value k∗ = 6, discovering new candidate communities. In addition to discovering large communities that partition entire chromosomes, we also show that CD can detect small-scale topologically associating domains (TADs) such as those found in Dixon, et al. (2012). CD thus provides a natural and flexible statistical framework for understanding the folding structure of DNA at multiple scales in Hi-C data.

Original languageEnglish (US)
Title of host publication2016 50th Annual Conference on Information Systems and Sciences, CISS 2016
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages584-589
Number of pages6
ISBN (Electronic)9781467394574
DOIs
StatePublished - Apr 26 2016
Event50th Annual Conference on Information Systems and Sciences, CISS 2016 - Princeton, United States
Duration: Mar 16 2016Mar 18 2016

Publication series

Name2016 50th Annual Conference on Information Systems and Sciences, CISS 2016

Other

Other50th Annual Conference on Information Systems and Sciences, CISS 2016
Country/TerritoryUnited States
CityPrinceton
Period3/16/163/18/16

All Science Journal Classification (ASJC) codes

  • Computer Networks and Communications
  • Information Systems

Keywords

  • Community Detection
  • DNA Folding
  • Hi-C
  • Mixed-Membership Models

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