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Figure 6 | BMC Bioinformatics

Figure 6

From: AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number

Figure 6

Genes significantly up-regulated in pluripotent stem cells. (A) Heat map representation of AutoSOME co-expression analysis of the microarray data GSE11508 [26] 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 [1] and the heat map was generated with Java TreeView [57]. (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 [31]). 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 [59] of Cytoscape 2.6.0 [34].

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