Table 2.
Significantly induced pathways associated with the response of primary epithelia to stroma co-culture in 3D
| Rank | Pathway | Impact Factor | no. genes/ genes in pathway | Upregulated genes | Downregulated genes |
|---|---|---|---|---|---|
| 1 | Cell adhesion molecules | 246.278 | 9/133 | CLDN22, CLDN6, HLA-DPB1, ITGB2, NRXN3, PTPRC | CD22, CLDN7, ITGA6 |
| 2 | Phosphatidyl inositol signalling | 27.591 | 4/77 | PRKCB1 | DGKG, INPP4B, PLCD3 |
| 3 | Antigen processing and presentation | 20.271 | 6/88 | HLADPB1, KLRC2, KLRC4, IFNA21, KIR3DL2 |
NFYB |
| 4 | Adherens junction | 10.67 | 2/75 | ACVR1B | PTPRB |
| 5 | Type II diabetes mellitus | 7.677 | 2/44 | CACNA1C, CACNA1E |
|
| 6 | Long term depression | 5.7 | 6/76 | GRM1, NPR2, PRKCB1 | CRHR1, HRAS, PLA2G6 |
| 7 | Gap junction | 5.297 | 8/96 | GRM1, HTR2, NPR2, PRKCB1, TUBB6 | HRAS,PRKACB |
| 8 | Tight junction | 5.253 | 10/135 | CLDN22, CLDN6, MYH10, MYH6, PRKCB1 | CLDN7, HRAS, MYH14, PP2R4, PRKCQ |
| 9 | Melanoma | 5.206 | 4/71 | FGF11, FGF2, FGF18 | HRAS |
| 10 | Basal cell carcinoma | 5.174 | 1/55 | FZD2 | |
| 11 | TGF beta signalling | 4.763 | 3/89 | ACVR1B, DCN | ZFYVE9 |
| 12 | Glioma | 4.756 | 4/64 | PRKCB1 | CAMK2D, HRAS, SHC2 |
| 13 | MAPK signalling pathway | 4.747 | 19/265 | CACNA1C, CACNA1E, CACNA1S, CACNB2, ACVR1B, FGF11, FGF2, FGF18, FOS, JUN, PAK1, PRKCB1 |
CRKL, HRAS, MAP3K7IP2, PLA2G6, PRKACB, PRKX |
The 'primary 1.1 fold gene list' was loaded into Pathway Express to determine the significant epithelial pathways associated with co-culture with stroma in 3D. The 1.1 fold gene list was derived from all ten primary epithelial cell cultures. All significantly (p < 0.05) ranked pathways are shown (91 ranked in total).