Resolving Spatial Inconsistencies in Chromosome Conformation Data

  • Geet Duggal
  • Rob Patro
  • Emre Sefer
  • Hao Wang
  • Darya Filippova
  • Samir Khuller
  • Carl Kingsford
Conference paper

DOI: 10.1007/978-3-642-33122-0_23

Part of the Lecture Notes in Computer Science book series (LNCS, volume 7534)
Cite this paper as:
Duggal G. et al. (2012) Resolving Spatial Inconsistencies in Chromosome Conformation Data. In: Raphael B., Tang J. (eds) Algorithms in Bioinformatics. WABI 2012. Lecture Notes in Computer Science, vol 7534. Springer, Berlin, Heidelberg

Abstract

We introduce a new method for filtering noisy 3C interactions that selects subsets of interactions that obey metric constraints of various strictness. We demonstrate that, although the problem is computationally hard, near-optimal results are often attainable in practice using well-designed heuristics and approximation algorithms. Further, we show that, compared with a standard technique, this metric filtering approach leads to (a) subgraphs with higher total statistical significance, (b) lower embedding error, (c) lower sensitivity to initial conditions of the embedding algorithm, and (d)  structures with better agreement with light microscopy measurements.

Keywords

metric subgraph chromosome conformation 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Geet Duggal
    • 1
  • Rob Patro
    • 1
  • Emre Sefer
    • 1
  • Hao Wang
    • 2
  • Darya Filippova
    • 1
  • Samir Khuller
    • 1
  • Carl Kingsford
    • 1
  1. 1.Department of Computer ScienceUniversity of MarylandCollege ParkUSA
  2. 2.Department of Electrical and Computer EngineeringUniversity of MarylandCollege ParkUSA

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