Detecting community structures in Hi-C genomic data

Irineo Cabreros, Emmanuel Abbe, Aristotelis Tsirigos

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

12 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
CountryUnited 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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  • Cite this

    Cabreros, I., Abbe, E., & Tsirigos, A. (2016). Detecting community structures in Hi-C genomic data. In 2016 50th Annual Conference on Information Systems and Sciences, CISS 2016 (pp. 584-589). [7460568] (2016 50th Annual Conference on Information Systems and Sciences, CISS 2016). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CISS.2016.7460568