title: Modified logistic regression models using gene coexpression and clinical features to predict prostate cancer progression.
abstract: Predicting disease progression is one of the most challenging problems in prostate cancer research. Adding gene expression data to prediction models that are based on clinical features has been proposed to improve accuracy. In the current study, we applied a logistic regression (LR) model combining clinical features and gene co-expression data to improve the accuracy of the prediction of prostate cancer progression. The top-scoring pair (TSP) method was used to select genes for the model. The proposed models not only preserved the basic properties of the TSP algorithm but also incorporated the clinical features into the prognostic models. Based on the statistical inference with the iterative cross validation, we demonstrated that prediction LR models that included genes selected by the TSP method provided better predictions of prostate cancer progression than those using clinical variables only and/or those that included genes selected by the one-gene-at-a-time approach. Thus, we conclude that TSP selection is a useful tool for feature (and/or gene) selection to use in prognostic models and our model also provides an alternative for predicting prostate cancer progression.
authors.affiliation: Industrial Center, Shenzhen Polytechnic, Shenzhen, Guangdong 518055, China ; Department of Genitourinary Medical Oncology, Unit 1374, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030-4009, USA.
authors.forename: Hongya
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Department of Genitourinary Medical Oncology, Unit 1374, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030-4009, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Logothetis
authors.affiliation: Department of Genitourinary Medical Oncology, Unit 1374, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030-4009, USA.
authors.forename: Ivan P
authors.initials: IP
authors.lastname: Gorlov
authors.affiliation: School of Computer Science and Technology, Soochow University, Suzhou 215006, China.
authors.forename: Jia
authors.initials: J
authors.lastname: Zeng
authors.affiliation: School of Applied Chemistry and Biotechnology, Shenzhen Polytechnic, Shenzhen, Guangdong 518055, China.
authors.forename: Jianguo
authors.initials: J
authors.lastname: Dai
mesh_terms: D000465:Algorithms; D019540:Area Under Curve; D019295:Computational Biology; D018076:DNA, Complementary / Q000378:metabolism; D018450:Disease Progression; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D005838:Genotype; D006801:Humans; D016015:Logistic Models; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D011336:Probability; D011379:Prognosis; D011471:Prostatic Neoplasms / Q000175:diagnosis* / Q000378:metabolism*
chemical_list: D018076:DNA, Complementary