Current Bioinformatics

Yi-Ping Phoebe Chen
Department of Computer Science and Information Technology
La Trobe University
Melbourne
Australia

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Quantifying Gene Co-Expression Heterogeneity in Cancer Towards Efficient Network Biomarker Design

Author(s): Shang Gao, Abdullah Sarhan, Reda Alhajj, Jon Rokne, Doug Demetrick, Jia Zeng.

Abstract:

It is well known that cancer is a highly heterogeneous disease, and the predictive capability of targeted gene signature approach suffers from the inter-tumor heterogeneity. Here we propose a framework to quantify the molecular heterogeneity of tumors from gene-gene relational perspective using co-expression networks and interactome data. We believe that to understand individualized gene behavior across patients, relational status of genes needs to be considered because complex disease phenotype is often caused by failures of genetic interactions in cancer cells.

We quantified gene-gene relational heterogeneity from a benchmark data set using co-expression networks inferred from Microarray data, and showed that genes related to breast cancer metastasis can be stratified to different classes based on their relational status obtained from pair-wise comparisons of co-expression networks. Further we used the relational heterogeneity information to predict patient survival and found that relationally heterogeneous gene set is less predictive than relatively conserved cancer genes. We explored heterogeneity gene sets using interactome data and identified densely connected components that are causal to inter-tumor heterogeneity. We independently validated our approach with two patient cohorts. Our results demonstrated the efficiency of using heterogeneity information to design network markers.

Keywords: Biomarkers, breast cancer, co-expression network, network biology, tumor heterogeneity.

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Article Details

VOLUME: 10
ISSUE: 3
Year: 2015
Page: [306 - 314]
Pages: 9
DOI: 10.2174/157489361003150723134952
Price: $58