PMID: 22174260Dec 17, 2011

Integrative network analysis to identify aberrant pathway networks in ovarian cancer

Pacific Symposium on Biocomputing
Li ChenIe-Ming Shih


Ovarian cancer is often called the 'silent killer' since it is difficult to have early detection and prognosis. Understanding the biological mechanism related to ovarian cancer becomes extremely important for the purpose of treatment. We propose an integrative framework to identify pathway related networks based on large-scale TCGA copy number data and gene expression profiles. The integrative approach first detects highly conserved copy number altered genes and regards them as seed genes, and then applies a network-based method to identify subnetworks that can differentiate gene expression patterns between different phenotypes of ovarian cancer patients. The identified subnetworks are further validated on an independent gene expression data set using a network-based classification method. The experimental results show that our approach can not only achieve good prediction performance across different data sets but also identify biological meaningful subnetworks involved in many signaling pathways related to ovarian cancer.

Related Concepts

Support Vector Machines
Biochemical Pathway
DNA Copy Number Changes
Kaplan-Meier Estimate
Ovarian Neoplasm
DNA, Neoplasm
Gene Expression
Ovarian Carcinoma
RNA, Neoplasm
Poly(A) Tail

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