P-values obtained by testing the Jensen-Shannon divergence in the spectra distributions among different laboratories.

<p>The tests were carried out under the null hypothesis, i.e., in typical development children datasets of different laboratories. The laboratories were numbered from one to seven and the p-values are after Bonferroni correction for multiple tests.</p

The frequency plots.

<p>The frequency plot for the eigenvalues of the eight species (<i>H. pylori</i>, <i>R. norvegicus</i>, <i>M. musculus</i>, <i>E. coli</i>, <i>C. elegans</i>, <i>S. cerevisiae</i>, <i>H. sapiens</i>, <i>D. melanogaster</i>).</p

Average parameters estimated by minimum distance estimator based on KL divergence for Erdös-Rényi random, scale-free, and small-world graphs.

<p> <b>One standard deviation is indicated between brackets. Calculations were carried out for 50 repetitions. The parameters to be estimated for each graph model are: the probability </b><b> of connecting two nodes for Erdös-Rényi graphs, the power of the preferential attachment </b><b> for scale-free graphs, and the rewiring probability </b><b> for small-world graphs.</b></p

The general characteristics of eight protein-protein interaction networks. For each network we indicate the number of nodes, the number of edges, the average degree, the diameter, the clustering coefficient and the average path length.

<p>The general characteristics of eight protein-protein interaction networks. For each network we indicate the number of nodes, the number of edges, the average degree, the diameter, the clustering coefficient and the average path length.</p

The estimated Kullback-Leibler divergence between the eight species and the three random graph models. In bold are the lowest KL divergence values.

<p>The estimated Kullback-Leibler divergence between the eight species and the three random graph models. In bold are the lowest KL divergence values.</p

ROC curve under the alternative hypothesis and p-value distribution under the null hypothesis.

<p>(<b>A</b>) Erdös-Rényi graphs; (<b>B</b>) scale-free graphs, and (<b>C</b>) small-world graphs. For the ROC curves, the x-axis represents the 1-specificity and the y-axis the sensitivity. Both ROC curves and p-value distributions were constructed by analyzing 10,000 experiments. Solid and dashed lines represent the test based on the spectral and degree distributions, respectively.</p

Figure illustrating the performance of the model selection approach as a function of number of nodes.

<p>Given a graph belonging to (<b>A</b>) Erdös-Rényi with parameter , (<b>B</b>) scale-free with parameter , and (<b>C</b>) small-world with parameter  = 0.3, the solid, dashed, and dotted lines represent the proportion of graphs classified as Erdös-Rényi, scale-free, and small-world, respectively. Notice that the larger is the graph, the higher is the proportion of correct hits, showing that the model selection approach is consistent. For each graph size (10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120 nodes), 1,000 repetitions were carried out.</p

Venn diagrams showing the number of common DE genes and the common enriched transcription factors across the experimental comparisons.

<p>(A) Number of common and exclusively regulated genes at 3 and 6 hours intervals for Ang x Control, Ang II+Los x Ang II and Ang II+PD123319 x Ang II comparisons. (B) Number and enriched transcription factors observed when each time interval was analyzed separately. (C) Number and enriched transcription factors observed for the same comparisons at both 3 and 6 hours time intervals.</p

List of top-ranked hubs identified in the transcriptional networks derived from Ang II v+ Los vs Ang 6 h, Ang II + PD123319 vs Ang II 3 h and Ang II + PD123319 vs Ang II 6 h comparisons.

<p>Top-ranked hubs were identified according to their betweenness centrality values and their relevance in tumor biology was determined. The main literature findings on cancer were highlighted for the top five differentially expressed (DE) genes and DE-related genes. Genes that co-express with DE genes (DE-related genes) were included in the networks to verify how DE genes interact with other functionally related genes.</p><p>List of top-ranked hubs identified in the transcriptional networks derived from Ang II v+ Los vs Ang 6 h, Ang II + PD123319 vs Ang II 3 h and Ang II + PD123319 vs Ang II 6 h comparisons.</p

Transcriptional network enrichment analysis of hub genes found at Ang II + Losartan x Ang II 3 h comparison.

<p>(A) Scatter plot of betweenness centrality versus degree for nodes obtained in the transcriptional network analysis. Differentially expressed (DE) genes are represented as red (up-regulated) or green (down-regulated) diamonds in the graphic. DE-related genes are represented as purple diamonds. (B) Transcriptional interaction subnetwork containing the 25 DE genes and 15 DE-related genes with the highest centrality values in each network. DE genes are represented as red (up-regulated) or green (down-regulated) squares in the networks. DE-related genes are represented as purple diamonds. Genes previously associated with the keywords “Angiotensin II” and “glioma” display yellow border colors. Genes previously associated with the keywords “glioma”, “migration” or “invasion” display sea green border colors. (C) KEGG categories showing enrichment in functions for the hub genes.</p