Table 2.
Highly aberrational pathways identified in our cutaneous squamous cell carcinoma (cSCC) cohort
| Pathway | Pathway ID | Pathlength | % Pathway with SNVs | % Pathway with CNVs |
|---|---|---|---|---|
| Inactivation, recovery, and regulation of the phototransduction cascade | R-HSA-2514859 | 33 | 30.30 | 18.18 |
| Eph-ephrin signaling | R-HSA-2682334 | 92 | 26.09 | 39.13 |
| Eph-ephrin mediated repulsion of cellsa | R-HSA-3928665 | 49 | 47.06 | 36.73 |
| EPHA-mediated growth cone collapse | R-HSA-3928663 | 15 | 37.93 | 46.67 |
Using HitWalker2, we identified high-priority genes based on their mutational burden in pathways that do not contain highly overlapping gene members. Pathway Names, IDs, and pathway size are provided from Reactome annotation. Percentage of the pathway with SNVs and CNVs were calculated by dividing the total number of proteins in the pathway by the number of unique genes with SNVs and CNVs respectively.
(SNV) Single-nucleotide variant, (CNV) copy-number variant. aIndicates daughter pathways within the parent Eph-ephrin signaling pathway.