Fig. 6. Transcriptome analysis of NANOG overexpressing cells. DNA microarray analysis was performed on RNA extracted from NANOG overexpressing cells, wild-type ES cells, EB2d, EB10d and EB30d. Analysis was performed using the U133A chip from Affymetrix, each experiment was performed in triplicate and each DNA microarray was normalized to an average value of 100. (A) Dendogram analysis reveals that upon overexpression of NANOG, the similarity of the cells to cells of EB2d increases. (B) Differentially expressed genes were divided into four groups: (I) genes upregulated in NANOG overexpressing cells and in EB2d compared with ES cells; (II) genes upregulated in NANOG overexpressing cells compared with both ES cells and EB2d; (III) genes downregulated in both NANOG overexpressing cells and in EB2d compared with ES cells; and (IV) genes downregulated in NANOG overexpressing cells compared with both ES cells and EB2d. (C) Shown are genes upregulated in NANOG overexpressing cells in comparison with wild-type ES cells. All the genes shown are at least fourfold upregulated in NANOG overexpressing cells. (D) Shown are genes downregulated in NANOG overexpressing cells in comparison with wild-type ES cells. All the genes shown are downregulated by at least 25-fold in NANOG overexpressing cells.