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Differential Expression Analysis for A Mouse p53KO Microarray Dataset

Affymetrix GeneChip technology is used to detect gene expression levels in samples of cells under different conditions. In this project, we analyzed the gene expression profiling data for mouse induced pluripotent stem cell (iPSCs) (Takahashi, 2006) on Affymetrix Mouse 430 2.0 GeneChip. Three biological conditions were present: p53KO, microRNA mir34aKO, and wild type, each with three biological replicates. The first part was devoted to identifying differentially expressed genes from around 45,000 of them, and looking into their biological meanings by pathway analysis. The second part dealt with repetitive elements represented in the pool of mRNAs. We identified repetitive elements that show a significant difference between two biological conditions. Both the comparison of p53KO versus WT and mir34aKO versus WT were done. However, the emphasis was on the former. Laboratory validation with qPCR confirmed our findings. This work was done under the Overseas Research Fellowship (ORF) Scheme 2012 for Science Students by the Faculty of Science, The University of Hong Kong. Many thanks are due to the University for the fellowship, and to Professors Terry Speed and Lin He and Drs Chao-po Lin and Anne Biton of the University of California at Berkeley for their supervision and generous support.