Figure 2

Pathways enriched among genes with high HT or T2D phenotype probabilities or differentially expressed genes. (A) Enriched pathways are listed according to their HT and T2D phenotype probabilities. The color in the heat plot indicates the normalized enrichment score given by the GSEA program. A black cell indicates that the pathway is not significantly changed in the analysis. For microarray expression analysis, the significantly up-regulated and down-regulated pathways are colored red and green, respectively. (B) Number of links between genes with high phenotype probabilities (> 95% specificity as determined in Fig. 4.) and those differentially expressed (RankProd pfp < 0.01) and its significance determined by Monte Carlo simulations. The red line indicates the number of interactions between the genes that have high phenotype probabilities (gene set A) and the genes only differentially expressed in various tissues combined (gene set B) as detected by microarray experiments. The black, blue or green curves indicate the probability density distributions of the number of links if genes in both set A and set B, either A (blue curve) or B (green curve) are replaced by randomly selected genes. Empirical P values are labeled on each graph. (C) Distribution of interaction degree k of high disease phenotype probability (> 95% specificity) genes (red curve), differentially expressed genes (green curve) and all genes in the interactome network (black curve). The Wilcoxon rank test P values of increase in k compared to the background 'all genes' are indicated for each gene set.