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Differentially Mutated Subnetworks Discovery

Authors Morteza Chalabi Hajkarim, Eli Upfal, Fabio Vandin

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Author Details

Morteza Chalabi Hajkarim
  • Biotech Research and Innovation Centre, University of Copenhagen, Denmark
Eli Upfal
  • Department of Computer Science, Brown University, Providence, RI, USA
Fabio Vandin
  • Department of Information Engineering, University of Padova, Italy

Funding

This work is supported, in part, by University of Padova project SID2017 and STARS: Algorithms for Inferential Data Mining, and by NSF grant IIS-1247581.
  • Vandin, Fabio: corresponding author

Cite As Get BibTex

Morteza Chalabi Hajkarim, Eli Upfal, and Fabio Vandin. Differentially Mutated Subnetworks Discovery. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 18:1-18:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018) https://doi.org/10.4230/LIPIcs.WABI.2018.18

Abstract

We study the problem of identifying differentially mutated subnetworks of a large gene-gene interaction network, that is, subnetworks that display a significant difference in mutation frequency in two sets of cancer samples. We formally define the associated computational problem and show that the problem is NP-hard. We propose a novel and efficient algorithm, called DAMOKLE to identify differentially mutated subnetworks given genome-wide mutation data for two sets of cancer samples. We prove that DAMOKLE identifies subnetworks with a statistically significant difference in mutation frequency when the data comes from a reasonable generative model, provided enough samples are available. We test DAMOKLE on simulated and real data, showing that DAMOKLE does indeed find subnetworks with significant differences in mutation frequency and that it provides novel insights not obtained by standard methods.

Subject Classification

ACM Subject Classification
  • Mathematics of computing → Graph algorithms
  • Applied computing → Biological networks
  • Applied computing → Computational genomics
Keywords
  • Cancer genomics
  • network analysis
  • combinatorial algorithm

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