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Updated: May 10, 2026
Discovery of Driver Genes in Colorectal HT29-derived Cancer Stem-Like Tumorspheres
Published on: July 22, 2020
Comprehensive detection of cancer gene expression profiles and gene networks are impacted by the choice of
N Baskaran1, Chee Keong Kwoh, Kam M Hui
1Bek Chai Heah Laboratory of Cancer Genomics, Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre, 11 Hospital Drive, Singapore 169610, Singapore. baskaran@nccs.com.sg
Abstract:
Pre-processing algorithms (PPA) and gene-selection methods (GSM) are commonly employed to select Differentially Expressed Genes (DEGs) from microarray data. Previous studies established that different combinations of PPAs and GSMs are intrinsically different in their performance to select biologically relevant DEGs. In this study, we evaluated eight combinations of PPAs and GSMs for their ability to select DEGs for prioritising gene-networks. Although the different combinations yielded dissimilar DEG-lists, all DEG-lists selected could segregate tumour from normal. Nevertheless, the DEG-list selected significantly impacted the prioritisation of cancer-associated gene-networks; hence the initial choice of PPA and GSM is crucial for subsequent interactome investigations.
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