Table 4.
Significant pathways associated with the response of BPH-1 cells to stroma in 3D culture
| Rank | Pathway Name | Impact Factor | no. genes/ genes in pathway | Upregulated genes | Downregulated genes |
|---|---|---|---|---|---|
| 1 | ECM-receptor interaction | 14.5* | 10/84 | COL6A1, LAMB2 | CD44, CD47, FN1, ITGA2, LAMB1, THBS1 |
| 2 | Adherens junction | 11.94 | 1/78 | MET | |
| 3 | Haematopoietic cell lineage | 9.93* | 8/87 | CD44, CD55. CD59, IL1R2, IL4R, IL7R, ITGA2, ITGA6 | |
| 4 | Small cell lung cancer | 7.96* | 7/86 | LAMB2 | FN1, ITGA2, ITGA6, LAMB1, MYC |
| 5 | Basal cell carcinoma | 7.83 | 2/55 | WNT10A, WNT4 | |
| 6 | Pathways in cancer | 7.27* | 13/330 | DAPK2, LAMB2, WNT10A, WNT4 | ETS1, FN1, ITGA2, ITGA6, LAMB1, MET, MYC, RUNX1 |
| 7 | Focal adhesion | 7.02* | 10/203 | COL6A1, LAMB2 | FLNB, FN1, ITGA2, LAMB1, MET, THBS1 |
| 8 | TGF-beta signalling pathway | 6.61* | 5/87 | INHBB | FST, MYC, THBS1, ID1 |
| 9 | Axon guidance | 6.48* | 7/129 | EFNB3, NFATC4, NTN1, SEMA3C | MET, PLXNC1, SRGAP1 |
| 10 | Jak-STAT signalling pathway | 6.32* | 7/155 | IL13RA2, IL24, IL4R, IL7R, MYC, OSMR, SOCS3 | |
| 11 | Calcium signalling pathway | 4.93 | 2/182 | EDNRA, HRH1 | |
| 12 | Bladder cancer | 4.74* | 3/42 | DAPK2 | MYC, THBS1 |
| 13 | B cell receptor signalling pathway | 4.62 | 2/65 | BLNK, NFATC4 | |
| 14 | Complement and coagulation cascades | 4.59* | 4/69 | C3 | CD55, CD59, F3 |
| 15 | Cytokine-cytokine receptor interaction | 4.56* | 9/263 | INHBB | CXCL5, IL1R2, IL24, IL4R, IL7R, MET, OSMR, PPBP |
| 16 | Regulation of actin cytoskeleton | 4.37 | 5/217 | CYFIP2 | FN1, ITGA2, ITGA6, SSH1 |
| 17 | Regulation of autophagy | 4.32 | 1/35 | GABARAPL1 | |
| 18 | Melanoma | 4.25 | 1/71 | MET | |
| 19 | Wnt signaling pathway | 4.2 | 4/152 | NFATC4, WNT10A, WNT4 | MYC |
| 20 | Tight junction | 4.11 | 2/135 | JAM2, TJP3 | |
The 'BPH1 1.1 fold gene list' was loaded into pathway express. All pathways with an impact factor > 4 are listed. * significant pathways, p < 0.05. The 1.1 fold gene list was derived from all three BPH-1 cultures.