Please use this identifier to cite or link to this item: https://hdl.handle.net/2440/131587
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Type: Journal article
Title: DriverGroup: a novel method for identifying driver gene groups
Author: Pham, V.V.H.
Liu, L.
Bracken, C.P.
Goodall, G.J.
Li, J.
Le, T.D.
Citation: Bioinformatics, 2020; 36(Supplement_2):i583-i591
Publisher: Oxford University Press
Issue Date: 2020
ISSN: 1367-4803
1367-4811
Statement of
Responsibility: 
Vu V H Pham, Lin Liu, Cameron P Bracken, Gregory J Goodall, Jiuyong Li, Thuc D Le
Abstract: Motivation Identifying cancer driver genes is a key task in cancer informatics. Most existing methods are focused on individual cancer drivers which regulate biological processes leading to cancer. However, the effect of a single gene may not be sufficient to drive cancer progression. Here, we hypothesize that there are driver gene groups that work in concert to regulate cancer, and we develop a novel computational method to detect those driver gene groups.<h4>Results</h4>We develop a novel method named DriverGroup to detect driver gene groups by using gene expression and gene interaction data. The proposed method has three stages: (i) constructing the gene network, (ii) discovering critical nodes of the constructed network and (iii) identifying driver gene groups based on the discovered critical nodes. Before evaluating the performance of DriverGroup in detecting cancer driver groups, we firstly assess its performance in detecting the influence of gene groups, a key step of DriverGroup. The application of DriverGroup to DREAM4 data demonstrates that it is more effective than other methods in detecting the regulation of gene groups. We then apply DriverGroup to the BRCA dataset to identify driver groups for breast cancer. The identified driver groups are promising as several group members are confirmed to be related to cancer in literature. We further use the predicted driver groups in survival analysis and the results show that the survival curves of patient subpopulations classified using the predicted driver groups are significantly differentiated, indicating the usefulness of DriverGroup. Availability and implementation DriverGroup is available at https://github.com/pvvhoang/DriverGroup. Supplementary information Supplementary data are available at Bioinformatics online.
Keywords: Humans
Breast Neoplasms
Mutation
Oncogenes
Gene Regulatory Networks
Rights: © The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com
DOI: 10.1093/bioinformatics/btaa797
Grant ID: http://purl.org/au-research/grants/arc/DP170101306
Appears in Collections:Aurora harvest 4
Physics publications

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