title: Integrating multidimensional omics data for cancer outcome.
abstract: In multidimensional cancer omics studies, one subject is profiled on multiple layers of omics activities. In this article, the goal is to integrate multiple types of omics measurements, identify markers, and build a model for cancer outcome. The proposed analysis is achieved in two steps. In the first step, we analyze the regulation among different types of omics measurements, through the construction of linear regulatory modules (LRMs). The LRMs have sound biological basis, and their construction differs from the existing analyses by modeling the regulation of sets of gene expressions (GEs) by sets of regulators. The construction is realized with the assistance of regularized singular value decomposition. In the second step, the proposed cancer outcome model includes the regulated GEs, "residuals" of GEs, and "residuals" of regulators, and we use regularized estimation to select relevant markers. Simulation shows that the proposed method outperforms the alternatives with more accurate marker identification. We analyze the The Cancer Genome Atlas data on cutaneous melanoma and lung adenocarcinoma and obtain meaningful results.
authors.affiliation: Department of Statistics, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
authors.forename: Ruoqing
authors.initials: R
authors.lastname: Zhu
authors.affiliation: Department of Biostatistics, Yale University, New Haven, CT, USA.
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhao
authors.affiliation: Department of Biostatistics, Yale University, New Haven, CT, USA.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Department of Biostatistics, Yale University, New Haven, CT, USA shuangge.ma@yale.edu.
authors.forename: Shuangge
authors.initials: S
authors.lastname: Ma
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D017063:Outcome Assessment, Health Care / Q000379:methods*
keywords: Integrated analysis; Multidimensional data; Regularized estimation and selection