Multiscale Identification of Topological Domains in Chromatin

  • Darya Filippova
  • Rob Patro
  • Geet Duggal
  • Carl Kingsford
Conference paper

DOI: 10.1007/978-3-642-40453-5_23

Part of the Lecture Notes in Computer Science book series (LNCS, volume 8126)
Cite this paper as:
Filippova D., Patro R., Duggal G., Kingsford C. (2013) Multiscale Identification of Topological Domains in Chromatin. In: Darling A., Stoye J. (eds) Algorithms in Bioinformatics. WABI 2013. Lecture Notes in Computer Science, vol 8126. Springer, Berlin, Heidelberg

Abstract

Recent chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types, are conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various resolutions by adjusting a single scale parameter. The identified novel domains are substantially different from domains reported previously and are highly enriched for insulating factor CTCF binding and histone modifications at the boundaries.

Keywords

chromosome conformation capture topological domains weighted interval scheduling 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Darya Filippova
    • 1
    • 2
  • Rob Patro
    • 2
  • Geet Duggal
    • 1
    • 2
  • Carl Kingsford
    • 2
  1. 1.Ph.D. Program in Computational BiologyJoint Carnegie Mellon University, University of PittsburghPittsburghUSA
  2. 2.Lane Center for Computational BiologyCarnegie Mellon UniversityPittsburghUSA

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