Figure 1

Flow chart of the microarray data analysis. To illustrate the procedure, we arbitrarily used a set of 8 genes, whose expression varies across 3 different pairwise experimental comparisons and whose corresponding proteins undergo a certain number of interactions. (A) Generating a set of networks based on pairwise comparisons of experimental conditions. The starting point for this procedure is an initial set of differentially regulated genes (Gene list). This gene list is used to generate a network where nodes are genes (or proteins), which are first connected by edges based on available protein-protein interaction information (PPIs, black lines). The network connectivity is further enriched by the addition of extra edges, which indicate that the expression of linked genes is correlated across all given experimental conditions (grey dashed lines). Thus, the latter is based on tracking expression correlation between genes in pairwise comparisons as shown in panel B. Finally, the layout of the network is organized using the Cytoscape plugin Cerebral. Here, nodes are organized based on their intracellular localization and their level of connectivity (PPI and expression correlation). (B) Dynamic visualization of network maps of pairwise comparisons. Nodes in the network maps are colored with a red-to-green gradient according to their expression values, along all the analyzed pairwise comparisons. Two different patterns (A and B) of gene expression behaviors emerge by moving between the different network panels (x, y, z). This can be greatly facilitated by generating a animation from these network panels. (C) Detected patterns can suggest biological interpretations and new hypothesis.