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Table 2 Significantly induced pathways associated with the response of primary epithelia to stroma co-culture in 3D

From: Stromal upregulation of lateral epithelial adhesions: Gene expression analysis of signalling pathways in prostate epithelium

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

  1. 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).