title: Integrative network analysis to identify aberrant pathway networks in ovarian cancer.
abstract: 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.
authors.affiliation: The Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA. lchen06@vt.edu
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.forename: Jianhua
authors.initials: J
authors.lastname: Xuan
authors.forename: Jinghua
authors.initials: J
authors.lastname: Gu
authors.forename: Yue
authors.initials: Y
authors.lastname: Wang
authors.forename: Zhen
authors.initials: Z
authors.lastname: Zhang
authors.forename: Tian-Li
authors.initials: TL
authors.lastname: Wang
authors.forename: Ie-Ming
authors.initials: IeM
authors.lastname: Shih
mesh_terms: D019295:Computational Biology; D056915:DNA Copy Number Variations; D004273:DNA, Neoplasm / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D053263:Gene Regulatory Networks; D006801:Humans; D053208:Kaplan-Meier Estimate; D008390:Markov Chains; D008957:Models, Genetic; D010051:Ovarian Neoplasms / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D012334:RNA, Neoplasm / Q000235:genetics; D060388:Support Vector Machine
chemical_list: D004273:DNA, Neoplasm; D012333:RNA, Messenger; D012334:RNA, Neoplasm