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BMC Cancer  2010 

Meta-analysis of archived DNA microarrays identifies genes regulated by hypoxia and involved in a metastatic phenotype in cancer cells

DOI: 10.1186/1471-2407-10-176

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Affymetrix datasets about metastasis and/or hypoxia were downloaded from GEO and ArrayExpress. AffyProbeMiner and GCRMA packages were used for pre-processing and the Window Welch t test was used for processing. Three approaches of meta-analysis were eventually used for the selection of genes of interest.Three complementary approaches were used, that eventually selected 183 genes of interest. Out of these 183 genes, 99, among which the well known JUNB, FOS and TP63, have already been described in the literature to be involved in cancer. Moreover, 39 genes of those, such as SERPINE1 and MMP7, are known to regulate metastasis. Twenty-one genes including VEGFA and ID2 have also been described to be involved in the response to hypoxia. Lastly, DAVID classified those 183 genes in 24 different pathways, among which 8 are directly related to cancer while 5 others are related to proliferation and cell motility. A negative control composed of 183 random genes failed to provide such results. Interestingly, 6 pathways retrieved by DAVID with the 183 genes of interest concern pathogen recognition and phagocytosis.The proposed methodology was able to find genes actually known to be involved in cancer, metastasis and hypoxia and, thus, we propose that the other genes selected based on the same methodology are of prime interest in the metastatic phenotype induced by hypoxia.One of the major causes of death by cancer is metastasis. Determining the mechanisms of metastasis initiation and growth should thus improve therapy. Cancer cells have developed many mechanisms to detach from the primary tumor, invade surrounding tissues, migrate and colonize distant organs. These mechanisms include changes in cell-cell and cell-matrix adhesion molecules, extracellular matrix degradation enzymes, cytoskeleton regulation factors and cell-cell communication through cytokines, for example [1]. Recently, high-throughput studies performed in several cancer cell lines identified specific metastasis pa


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