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BioMed Research International
Volume 2017 (2017), Article ID 1016305, 8 pages
https://doi.org/10.1155/2017/1016305
Research Article

Identification of Pharmacologically Tractable Protein Complexes in Cancer Using the R-Based Network Clustering and Visualization Program MCODER

1Graduate Programs for Nanomedical Science, Yonsei University, Seoul, Republic of Korea
2Severance Biomedical Science Institute, Brain Korea 21 Plus Project for Medical Science, Yonsei University, College of Medicine, Seoul, Republic of Korea

Correspondence should be addressed to Hyun Seok Kim; ca.shuy@mikfsh

Received 3 March 2017; Revised 21 April 2017; Accepted 23 May 2017; Published 13 June 2017

Academic Editor: Xingming Zhao

Copyright © 2017 Sungjin Kwon et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Current multiomics assay platforms facilitate systematic identification of functional entities that are mappable in a biological network, and computational methods that are better able to detect densely connected clusters of signals within a biological network are considered increasingly important. One of the most famous algorithms for detecting network subclusters is Molecular Complex Detection (MCODE). MCODE, however, is limited in simultaneous analyses of multiple, large-scale data sets, since it runs on the Cytoscape platform, which requires extensive computational resources and has limited coding flexibility. In the present study, we implemented the MCODE algorithm in R programming language and developed a related package, which we called MCODER. We found the MCODER package to be particularly useful in analyzing multiple omics data sets simultaneously within the R framework. Thus, we applied MCODER to detect pharmacologically tractable protein-protein interactions selectively elevated in molecular subtypes of ovarian and colorectal tumors. In doing so, we found that a single molecular subtype representing epithelial-mesenchymal transition in both cancer types exhibited enhanced production of the collagen-integrin protein complex. These results suggest that tumors of this molecular subtype could be susceptible to pharmacological inhibition of integrin signaling.