Workshop: Algorithms for discovery of mutated pathways in cancer

Fabio Vandin, Eli Upfal, Benjamin J. Raphael

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

Abstract

We apply our algorithms to several cancer types including glioblastoma multiforme (GBM), lung adenocarcinoma, and ovarian carcinoma (OV). HotNet identifies significant subnetworks that are part of well-known cancer pathways as well as novel subnetworks. Among the most significant subnetworks identified in OV data is the Notch signaling pathway, and this result appears in the first TCGA OV publication [1]. We also extend HotNet to identify mutated pathways associated with patient survival [2]. In the TCGA OV data, we discover 9 subnetworks containing genes whose mutations are associated with survival. Genes in 4 of these subnetworks overlap pathways known to be associated to survival, including focal adhesion and cell adhesion pathways. In GBM and lung Dendrix finds significant sets of genes that are mutated in large subsets of patients and whose mutations are approximately exclusive, including genes in well known cancer pathways (e.g., Rb1 and p53 pathways).

Original languageEnglish (US)
Title of host publication2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012
DOIs
StatePublished - May 8 2012
Externally publishedYes
Event2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012 - Las Vegas, NV, United States
Duration: Feb 23 2012Feb 25 2012

Publication series

Name2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012

Other

Other2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012
CountryUnited States
CityLas Vegas, NV
Period2/23/122/25/12

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Applied Mathematics

Keywords

  • Markov chain Monte Carlo
  • cancer genomics
  • diffusion processes
  • driver pathways
  • networks

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