Table 1. Sub networks from the HER2-positive tumor interactome model.
| Module | Pathway | Number of Genes in Module | Number of Genes in Pathway | P-value | FDR Pathway Enrichment | Nodal Genes in Pathway |
|---|---|---|---|---|---|---|
| 1 | Aurora A signaling (N) | 44 | 6 | 0 | <1.00e-03 | CYLD, BCL3, CHUK, RELA, TP53, BIRC2 |
| 2 | Integrin signaling pathway (P) | 33 | 10 | 0 | <1.00e-03 | CAV1, ACTG1, LAMB2, ITGAX, ARPC2, ITGAV, COL6A2 ,FLNB, FYN, ABL1 |
| 3 | Phosphatidyl-inositol signaling system(K) | 33 | 7 | 0 | <1.00e-03 | PIP5K1C, PLCB4, PIK3CA, INPP5E, PIK3R1, DGKQ, INPP4A |
| 4 | Transport of Mature Transcript to Cytoplasm (R) | 27 | 10 | 0 | <1.00e-03 | NUP214, CDC40, NUP54, RANBP2, TPR, NUP133, NUPL2, UPF3B, NUP205, NUP107 |
| 5 | Signaling by NGF(R) | 24 | 8 | 0 | <1.00e-03 | PPP2R1B, RTN4, CREB1, FOXO1, ATF1, GSK3B, PRKACA, AKT2 |
| 6 | FOXA1 transcription factor network (N) | 23 | 2 | 0.0009 | 2.26E-01 | FOXA1, NR2F2 |
| 7 | Ubiquitin mediated proteolysis (K) | 17 | 5 | 0 | <1.00e-03 | UBE3A, ANAPC10, STUB1, UBE2D1, UBE2E1 |
| 8 | Signaling by Rho GTPases (R) | 9 | 6 | 0 | <1.00e-03 | TAGAP, PLEKHG2, RHOT2, ARHGEF17, AKAP13, ARAP2 |
| 9 | G2/M Transition (R) | 9 | 5 | 0 | <1.00e-03 | PLK4, CEP57, CKAP5, ALMS1, TUBA1A |
| 10 | M Phase (R) | 8 | 3 | 0 | <1.00e-03 | SMC3, STAG2, STAG1 |
| 11 | Insulin Synthesis and Secretion (R) | 7 | 3 | 0 | 1.00E-03 | SRP54, TRAM1, SSR1 |
| 12 | TGF-beta receptor signaling | 6 | 4 | 0 | <1.00e-03 | SNX6, TGFBR1, YAP1, ENG |
The interactome model identified 12 discrete modules or sub-networks. The total number of genes in each module as well as key nodal genes within each module are given below.