Table 2 Pathway over-representation analysis using the 232 genes for which the 251 probes showing pre-afatinib cell-free DNA (cfDNA) methylation profiles correlated with progression-free survival (PFS) are designed, based on the protein analysis using the evolutionary relationships database (version 18.0, https://www.pantherdb.org) (P < 0.05 and false discovery rate [FDR] < 0.1)
ID | Description | P | FDR | Genes for which cfDNA methylation status was correlated with PFS and are involved in the pathway |
|---|---|---|---|---|
P00012 | Cadherin signaling pathway | 2.06 × 10–4 | 2.43 × 10–3 | PCDHGA2, PCDHGB2, PCDHGA1, PCDHGB1, CDH6, CTNNA2, PCDHGA5, PCDHGA3 |
P00057 | Wnt signaling pathway | 2.21 × 10–4 | 2.43 × 10–3 | PCDHGA2, PCDHGB2, PCDHGA1, PCDHGB1, CDH6, NKD2, CTNNA2, SMARCA2, PLCB4, PCDHGA5, PCDHGA3 |
P00018 | EGF receptor signaling pathway | 2.05 × 10–3 | 1.51 × 10–2 | PIK3C2A, PIK3R6, CCM2, PLCB4, TGFA, PHLDB2 |
P00019 | Endothelin signaling pathway | 1.05 × 10–2 | 5.76 × 10–2 | PRKG1, PIK3C2A, PIK3R6, PLCB4 |
P00060 | Ubiquitin proteasome pathway | 1.91 × 10–2 | 7.33 × 10–2 | PSMD6, WWP1, UBE2H |
P04391 | Oxytocin receptor mediated signaling pathway | 2.00 × 10–2 | 7.33 × 10–2 | PLCB4, CACNA1C, CACNA1D |
P04374 | 5HT2 type receptor mediated signaling pathway | 2.78 × 10–2 | 8.75 × 10–2 | PLCB4, CACNA1C, CACNA1D |