title: A prognostic model for the combined analysis of gene expression profiling in hepatocellular carcinoma.
abstract: Microarray techniques using cDNA array and comparative genomic hybridization (CGH) have been developed for several discovery applications. They are frequently applied for the prediction and diagnosis of cancer in recent years. Many studies have shown that integrating genomic data from different sources may increase the reliability of gene expression analysis results in understanding cancer progression. Therefore, developing a good prognostic model dealing simultaneously with different types of dataset is important. The challenge with these types of data is high background noise. We describe an analytical two-stage framework with a multi-parallel data analysis method named wavelet-based generalized singular value decomposition and shaving method (WGSVD-shaving). This method is proposed for de-noising and dimension-reduction during early stage prognosis modeling. We also applied a supervised gene clustering technique with penalized logistic regression with Cox-model on an integrated data. We show the accuracy of the method using a simulated dataset with a case study on Hepatocelluar Carcinoma (HCC) cDNA and CGH data. The method shows improved results from GSVD-shaving and has application in the discovery of candidate genes associated with cancer.
authors.affiliation: Centre for Clinical Trials, School of Public Health, Chinese University of Hong Kong, Shatin, Hong Kong SAR. bzee@cct.cuhk.edu.hk
authors.forename: Zee Chung Ying
authors.initials: ZC
authors.lastname: Benny
authors.forename: Lee Jock Wai
authors.initials: LJ
authors.lastname: Jack
authors.forename: Wong
authors.initials: W
authors.lastname: Nathalie
authors.forename: Yeo
authors.initials: Y
authors.lastname: Winnie
authors.forename: Lai Bo San
authors.initials: LB
authors.lastname: Paul
authors.forename: Mok Shu Kam
authors.initials: MS
authors.lastname: Tony
authors.forename: Chan Tak Cheung
authors.initials: CT
authors.lastname: Anthony
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