Genes significantly up-regulated in pluripotent stem cells. (A) Heat map representation of AutoSOME co-expression analysis of the microarray data GSE11508  showing all gene expression clusters. The heat map is ordered from left to right by decreasing cluster size, and hierarchically ordered from top to bottom by whole-transcriptome expression. EB, embryoid bodies (purple); TSC, teratocarcinoma cells (green); HUVEC, human umbilical vein endothelial cells (pink); [MSC, Fib, Ast], mesenchymal cells, fibroblasts, and astrocytes (light gray); SD-N, surgically-derived neural progenitors (dark gray); ESC-N, embryonic stem cells differentiated into neural stem cells (light blue); TSC-N, teratocarcinoma cells differentiated into dopaminergic neurons (dark blue); [F, PM-N], fetal and post-mortem feeder cells (brown); iPS, undifferentiated induced pluripotent stem cells (orange); ESC, undifferentiated embryonic stem cells (yellow); GCT, germ cell tumor cells (black). Cluster No. 1 represents genes up-regulated primarily in pluripotent stem cells (PluriUp). Several other clusters are labeled below the heat map. Cell lines were hierarchically reordered using Cluster software  and the heat map was generated with Java TreeView . (B) Venn diagram demonstrating that the PluriUp gene cluster shares 256 genes with PluriNet, a highly significant overlap as determined by Fisher's Exact Test (p < 10-15). (C) The highly interconnected protein-protein interaction network called PluriPlus, consisting of 1165 PluriUp genes, is illustrated as a network diagram. Genes are positioned in the network according to subcellular localization (Gene Ontology from Human Protein Reference Database ). Genes found in both PluriUp and PluriNet are colored purple, and genes found exclusively in PluriUp are colored blue. The network diagram was generated using the Cerebral plugin  of Cytoscape 2.6.0 .