We provide toy-examples to illustrate the parameters e.g. weight score, traversal path, and network topology's potential effects on WIPER ranking.

I. The initial edge weight effects the WIPER score, but not the Usage Fold-Change(UFC) score.

Fig. S1. The edge weight's effect given input as 0.5, 0.7, and 0.9 on the WIPER score.

II. The edge traversal path effects the WIPER score, but again, not the UFC score.

Fig. S2. The edge traversal path length's effect on the WIPER score.

III. The UFC score provides a ranking by finding out the central edges and the peripheral edges purely based on the network's topology.

Fig. S3. The network topology's effect on the WIPER score.

IV. The UFC score provides equal ranking in the centrosymmetric topology, and ordered ranking in the axisymmetric topology.

Fig. S4. The network topology symmetry's effect on the WIPER score.

We provide 17 case studies of KEGG pathways in different diseases. The material can be accessed by click here.