A pathway viewer has been developed in order to make easier the visualization of the comparison results.

You can select the pathway to see in the Categories list (1). You can also visualize a single circuit by clicking on its name (3) in the Circuits list (2). Circuits depicted in blue are significantly down-regulated circuits whereas those depicted in red are significantly up-regulated ones (p-value = 0.05). Circuits depicted in grey are not significant.

The information summarized in the pathway viewer includes:

Node's shape:

• Ellipses correspond to genes.
• Circles represent metabolites.
• Rectangles are cellular functions.

Node's color:

• Blue for down-regulated genes, red for up-regulated genes and grey for not significant genes.
• The intensity of the color depends on the significance of the differential expression.

Edge's shape: Edges represent either activations or inhibitions.

• Activations are represented by classic arrows.
• Inhibitions are represented by T arrows.

Edge's color:

• Circuits which are up-regulated in the disease condition have their arrows colored in red.
• Circuits which are down-regulated in the disease condition have their arrows colored in blue.
• Circuits which are not significant for the test have their arrows colored in grey.
• When an edge belongs to different circuits which should be colored in different colors, different arrows are depicted, each one for each necessary color.