Title: Estimating functional coupling between cancer gene sub-networks using novel interaction measures

Authors: Rama Srikanth Mallavarapu; Tae-Jin Ahn; Subhankar Mukherjee; Ajit S. Bopardikar; Garima Agarwal; Taesung Park

Addresses: SAIT-India, Samsung R&D Institute India, Bangalore, India ' Samsung Biomedical Research Institute, Samsung Electronics, South Korea ' Samsung R&D Institute India, Bangalore, India ' SAIT-India, Samsung R&D Institute India, Bangalore, India ' SAIT-India, Samsung R&D Institute India, Bangalore, India ' Department of Statistics, Seoul National University, Seoul, South Korea

Abstract: Cancer is a heterogeneous disease in that a single therapy may not be suitable for every patient. This is because, even within a single cancer, gene-level aberrations vary across patients. However, when genes are viewed at sub-network level, it is observed that these aberrations occur in sub-networks that are conserved across patients. Investigation of cancer gene sub-networks is therefore expected to yield greater insights. Also, multiple sub-networks could be involved in propagation of cancer and therefore coupling between them is of great importance. We present a method to measure and quantify coupling between two given sub-networks. For this we present interaction measures based on connecting genes and common neighbourhoods between sub-networks. We demonstrate this method using breast cancer focused around MET pathway and discuss functional coupling of various associated sub-networks. Studies based on such methods will play an important role in patient stratification and development of effective targeted therapies.

Keywords: cancer gene sub-networks; graph theory; sub-network analysis; genomic pathway analysis; data mining; functional coupling; cancer genes; interaction measures; breast cancer; patient stratification; bioinformatics.

DOI: 10.1504/IJDMB.2016.076002

International Journal of Data Mining and Bioinformatics, 2016 Vol.15 No.1, pp.10 - 21

Received: 31 Jan 2015
Accepted: 31 Jan 2015
Published online: 21 Apr 2016 *

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