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Fig. 4 | BioData Mining

Fig. 4

From: PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia

Fig. 4

A web application used to analyze pathway-pathway relationships in the eADAGE-based, P. aeruginosa KEGG network. a A user clicks on an edge (a pathway-pathway relationship) in the network visualization. b The user is directed to a page that displays expression data from the original transcriptomic dataset specific to the selected edge ( The expression data is visualized as two heatmaps that indicate the fifteen most and fifteen least expressed samples corresponding to the edge. To select the “most” and “least” expressed samples, we assign each sample a summary “expression score.” The expression score is based on the expression values of the genes (limited to the top twenty genes with an odds ratio above 1) annotated to one or both of the pathways. Here, we show the heatmap of least expressed samples specific to the [Phosphate transport - Type II general secretion] relationship. c Clicking on a square in the heatmap directs a user to an experiment page ( based on the sample corresponding to that square. A user can use the experiment page to identify whether the expression values of genes specific to an edge and a selected sample differ from those recorded in other samples of the experiment. In this experiment page, the first three samples (labeled in black) are P. aeruginosa “baseline” replicates grown for 72 h in drop-flow biofilm reactors. The following three samples (labeled in blue) are P. aeruginosa grown for an additional 12 h (84 h total). Labels in blue indicate that the three 84 h replicates are in the heatmap of least expressed samples displayed on the [Phosphate transport – Type II general secretion] edge page.

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