title: Network-based identification of reliable bio-markers for cancers.
abstract: Finding bio-markers for complex disease from gene expression profiles attracts extensive attentions for its potential use in diagnosis, therapy, and drug design. In this paper we propose a network-based method to seek high-confident bio-markers from candidate genes collected in the literature. The algorithm includes three consequent steps. First, one can collect the proposed bio-markers in literature as being the preliminary candidate; Second, a spanning-tree based threshold can be used to reconstruct gene networks for normal and cancer samples; Third, by jointly using of degree changes and distribution of the candidates in communities, one can filter out the low-confident genes. The survival candidates are high-confident genes. Specially, we consider expression profiles for carcinoma of colon. A total of 34 preliminary bio-markers collected from literature are evaluated and a set of 16 genes are proposed as high confident bio-markers, which behave high performance in distinguishing normal and cancer samples.
authors.affiliation: Business School, University of Shanghai for Science and Technology,Shanghai 200093, China.
authors.forename: Shiguo
authors.initials: S
authors.lastname: Deng
authors.affiliation: Business School, University of Shanghai for Science and Technology,Shanghai 200093, China.
authors.forename: Jingchao
authors.initials: J
authors.lastname: Qi
authors.affiliation: Business School, University of Shanghai for Science and Technology,Shanghai 200093, China; Computer Science Department, Masinde Muliro University of Science and Technology, P.O. Box 190-50100, Kakamega, Kenya.
authors.forename: Mutua
authors.initials: M
authors.lastname: Stephen
authors.affiliation: Business School, University of Shanghai for Science and Technology,Shanghai 200093, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Qiu
authors.affiliation: Business School, University of Shanghai for Science and Technology,Shanghai 200093, China. Electronic address: hjyang@ustc.edu.cn.
authors.forename: Huijie
authors.initials: H
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism*; D003110:Colonic Neoplasms / Q000175:diagnosis* / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D053263:Gene Regulatory Networks; D006801:Humans
chemical_list: D014408:Biomarkers, Tumor
keywords: Bio-marker; Complex network; Gene expressions