title: Mining gene link information for survival pathway hunting.
abstract: This study proposes a gene link-based method for survival time-related pathway hunting. In this method, the authors incorporate gene link information to estimate how a pathway is associated with cancer patient's survival time. Specifically, a gene link-based Cox proportional hazard model (Link-Cox) is established, in which two linked genes are considered together to represent a link variable and the association of the link with survival time is assessed using Cox proportional hazard model. On the basis of the Link-Cox model, the authors formulate a new statistic for measuring the association of a pathway with survival time of cancer patients, referred to as pathway survival score (PSS), by summarising survival significance over all the gene links in the pathway, and devise a permutation test to test the significance of an observed PSS. To evaluate the proposed method, the authors applied it to simulation data and two publicly available real-world gene expression data sets. Extensive comparisons with previous methods show the effectiveness and efficiency of the proposed method for survival pathway hunting.
authors.affiliation: School of Mechanical and Automotive Engineering, Hefei University of Technology, Hefei, People's Republic of China.
authors.forename: Gao-Jian
authors.initials: GJ
authors.lastname: Jing
authors.affiliation: School of Mechanical and Automotive Engineering, Hefei University of Technology, Hefei, People's Republic of China.
authors.forename: Zirui
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Machine Intelligence & Computational Biology Lab, Institute of Intelligent Machines, Chinese Academy of Sciences, P.O. Box 1130, Hefei, Anhui 230031, People's Republic of China.
authors.forename: Hong-Qiang
authors.initials: HQ
authors.lastname: Wang
authors.affiliation: School of Mechanical and Automotive Engineering, Hefei University of Technology, Hefei, People's Republic of China. hongmeizh@163.com.
authors.forename: Hong-Mei
authors.initials: HM
authors.lastname: Zheng
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis*; D057225:Data Mining / Q000379:methods*; D008040:Genetic Linkage; D006801:Humans; D009369:Neoplasms / Q000378:metabolism* / Q000401:mortality*; D015995:Prevalence; D011379:Prognosis; D016016:Proportional Hazards Models; D015203:Reproducibility of Results; D018570:Risk Assessment / Q000379:methods; D012680:Sensitivity and Specificity; D016019:Survival Analysis; D015996:Survival Rate
chemical_list: D014408:Biomarkers, Tumor