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Full-Text Articles in Physical Sciences and Mathematics
Measures For The Degree Of Overlap Of Gene Signatures And Applications To Tcga, Shuangge Ma
Measures For The Degree Of Overlap Of Gene Signatures And Applications To Tcga, Shuangge Ma
Shuangge Ma
For cancer and many other complex diseases, a large number of gene signatures have been generated. In this study, we use cancer as an example and note that other diseases can be analyzed in a similar manner. For signatures generated in multiple studies on the same cancer type/outcome, and for signatures on different cancer types, it is of interest to evaluate their degree of overlap. Many of the existing studies simply count the number (or percentage) of overlapped genes shared by two signatures. Such an approach has serious limitations. In this study, as a demonstrating example, we consider cancer prognosis …
Integrative Analysis Of High-Throughput Cancer Studies With Contrasted Penalization, Shuangge Ma
Integrative Analysis Of High-Throughput Cancer Studies With Contrasted Penalization, Shuangge Ma
Shuangge Ma
In cancer studies with high-throughput genetic and genomic measurements, integrative analysis provides a way to effectively pool and analyze heterogeneous raw data from multiple independent studies and outperforms ``classic" meta-analysis and single-dataset analysis. When marker selection is of interest, the genetic basis of multiple datasets can be described using the homogeneity model or the heterogeneity model. In this study, we consider marker selection under the heterogeneity model, which includes the homogeneity model as a special case and can be more flexible. Penalization methods have been developed in the literature for marker selection. This study advances from the published ones by …