title: Classifying ten types of major cancers based on reverse phase protein array profiles.
abstract: Gathering vast data sets of cancer genomes requires more efficient and autonomous procedures to classify cancer types and to discover a few essential genes to distinguish different cancers. Because protein expression is more stable than gene expression, we chose reverse phase protein array (RPPA) data, a powerful and robust antibody-based high-throughput approach for targeted proteomics, to perform our research. In this study, we proposed a computational framework to classify the patient samples into ten major cancer types based on the RPPA data using the SMO (Sequential minimal optimization) method. A careful feature selection procedure was employed to select 23 important proteins from the total of 187 proteins by mRMR (minimum Redundancy Maximum Relevance Feature Selection) and IFS (Incremental Feature Selection) on the training set. By using the 23 proteins, we successfully classified the ten cancer types with an MCC (Matthews Correlation Coefficient) of 0.904 on the training set, evaluated by 10-fold cross-validation, and an MCC of 0.936 on an independent test set. Further analysis of these 23 proteins was performed. Most of these proteins can present the hallmarks of cancer; Chk2, for example, plays an important role in the proliferation of cancer cells. Our analysis of these 23 proteins lends credence to the importance of these genes as indicators of cancer classification. We also believe our methods and findings may shed light on the discoveries of specific biomarkers of different types of cancers.
authors.affiliation: The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China.
authors.forename: Pei-Wei
authors.initials: PW
authors.lastname: Zhang
authors.affiliation: College of Information Engineering, Shanghai Maritime University, Shanghai, P.R. China.
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.affiliation: The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China.
authors.forename: Tao
authors.initials: T
authors.lastname: Huang
authors.affiliation: Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement, Tianjin University, Tianjin, P.R. China.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China.
authors.forename: Xiang-Yin
authors.initials: XY
authors.lastname: Kong
authors.affiliation: College of Life Science, Shanghai University, Shanghai, P.R. China.
authors.forename: Yu-Dong
authors.initials: YD
authors.lastname: Cai
mesh_terms: D019295:Computational Biology / Q000379:methods; D006801:Humans; D009369:Neoplasms / Q000378:metabolism*; D040081:Protein Array Analysis / Q000379:methods; D011506:Proteins / Q000378:metabolism*; D020543:Proteome / Q000378:metabolism
chemical_list: D011506:Proteins; D020543:Proteome
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