TY - GEN
T1 - Workshop
T2 - 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012
AU - Vandin, Fabio
AU - Upfal, Eli
AU - Raphael, Benjamin J.
PY - 2012/5/8
Y1 - 2012/5/8
N2 - 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).
AB - 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).
KW - Markov chain Monte Carlo
KW - cancer genomics
KW - diffusion processes
KW - driver pathways
KW - networks
UR - http://www.scopus.com/inward/record.url?scp=84860517158&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84860517158&partnerID=8YFLogxK
U2 - 10.1109/ICCABS.2012.6182678
DO - 10.1109/ICCABS.2012.6182678
M3 - Conference contribution
AN - SCOPUS:84860517158
SN - 9781467313216
T3 - 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012
BT - 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012
Y2 - 23 February 2012 through 25 February 2012
ER -