Table 9.
Enrichment analysis of the top scored subnetworks
| Stage | Biological Process | p-value | Genes in subnetworks |
|---|---|---|---|
| Common across all Stages |
Activation of MAPKK activity |
1.12E-03 |
PHOX2A*, HAND2*, PPP2R5D, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF, RAP1A |
| I & II |
Co-SMAD binding |
1.2E-05 |
FOXG1*, FOXH1, SMAD2, SMAD1, MED15, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF, RAP1A |
| II & III |
Nerve growth factor receptor signaling pathways |
2.21E-04 |
HOXD4*, INPP5B, SLC6A2, STX1A, VAMP1, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF, RAPIA |
| I & III |
Positive regulation of peptidyl-serine phosphorylation |
1.42E-03 |
NPY*, NPY1R, LSM7, NR1H2, RMI1, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF |
| I |
Transmembrane receptor protein tyrosine kinase signaling pathway |
1.87E-03 |
HLA-G*, COPB1, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF, RAP1A |
| II |
DNA helicase complex |
6.8E-05 |
SERPINB5*, UCHL5, ACTR8, ACTR5, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF |
| III | Nerve growth factor receptor signaling pathway | 5.5E-04 | HOXB4*, CREBBP, KLF13, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF, RAP1A |
*: commonality with Table 2.