| Pathways | Original | ARCH residuals | ||
| Number | Gene symbol | Number | Gene symbol | |
| ERBB2 signaling | 7 | ERBB2, KIT, NRG1 | 6 | ERBB2 |
| EGFR pathways | 11 | FLT1, KIT, PIK3R1, VAV3 | 10 | ERBB2, FLT1, PIK3R1 |
| Cell cycle | 5 | CDH1, MCM3 | 3 | MCM3, NUMA1 |
| Immune system | 5 | CDH1, KIT, PIK3R1, STAT6 | 5 | ERBB2, IFI6, STAT6 |
| Metabolic disorder | 1 | SAT1 | 1 | FZD1 |
| PI3K/AKT signaling | 5 | KIT, PIK3R1 | 5 | ERBB2, PIK3R1 |
| Wnt pathway | 5 | FZD1 | 5 | FZD1 |