Title: Gene co-expression analysis predicts genetic aberration loci associated with colon cancer metastasis

Authors: Jie Zhang; Shiwei Ni; Yang Xiang; Jeffrey D. Parvin; Yufeng Yang; Yongjian Zhou; Kun Huang

Addresses: Comprehensive Cancer Center, Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH 43201, USA ' Life Science Research Institute, Fuzhou University, Fuzhou, Fujian Province, 350108, China ' Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43201, USA ' Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43201, USA; Comprehensive Cancer Center, Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH 43201, USA ' Life Science Research Institute, Fuzhou University, Fuzhou, Fujian Province, 350108, China ' Concord Hospital, Fujian Medical University, Fuzhou, Fujian Province, 350001, China ' Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43201, USA; Comprehensive Cancer Center, Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH 43201, USA

Abstract: Gene Co-expression Network (GCN) analysis has been widely used for gene function and disease biomarker discovery. In this study, we present a workflow for identifying GCN associated with colon cancer metastasis. The workflow includes dense network discovery from weighted GCN followed by network activity analysis using a mutual information-based approach to identify gene networks related to metastasis. Our findings suggest several genomic regions as genetic aberrations related to colon cancer malignancy including chr11q13, 20q13, 8q24 and 14q22-23. Our work also demonstrates a novel way of interpreting gene co-expression analysis results besides functional relationships and the effectiveness of the mutual information based network analysis in detecting subtle changes between different disease states.

Keywords: GCN; gene co-expression networks; quasi-clique; network mining; colon cancer metastasis; copy number variation; cancer genome hotspot; genetic aberration loci; gene networks.

DOI: 10.1504/IJCBDD.2013.052202

International Journal of Computational Biology and Drug Design, 2013 Vol.6 No.1/2, pp.60 - 71

Published online: 20 Feb 2013 *

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