Fig. 1.

CluePedia analysis example using expression data from human normal colon mucosa and colorectal tumors and in silico information. (a) Functionally grouped network with pathways and genes. Terms are linked based on κ score (≥0.3). Edges show known activation (green), expression (yellow), post-translational modification (pink) and binding (blue). The edge thickness is scaled between the minimum and maximum scores shown. Terms and their associated genes share the color. ‘Regulation of IFNG signaling’ pathway is investigated in a subnetwork. (b) Genes not included in the initial selection are colored in white. Known interactions are shown. (c) Gene interrelations in normal samples are shown as Pearson correlation (blue) and MIC (orange), all values >0.7. Normalized expression data from five normal colon samples are shown as node label for IFNGR1 and IFNGR2. All spots corresponding to a gene are shown. (d) Pathway-like view of the network showing cellular locations. (e) ‘Regulation of IFNG signaling’ after enrichment steps. Five strongest correlating genes (Pearson) in normal colon and tumors, as well as the top five validated and predicted miRNAs (prediction score) are shown in blue, red, brown and beige, respectively. Negative correlations are shown as sinusoidal lines