Table 4.
Functional classification clustering analysis: genes differentially expressed in prostate cancer epithelial and stromal cells
| Gene functional classificationa | Number of genes (%)b | Gene symbols | Enrichment scores range |
|---|---|---|---|
| I. Gene clusters upregulated in epithelial cells (40 clustered genes)c | |||
| Group 1. Membrane-associated glycoproteins (including proteases) |
26 (65%) | ALCAM, AQP3, C1ORF115, C20ORF3, CLDN8, DPP4, FAM134A, FXYD3, GOLM1, GPR56, HPN, KLK2, KLK3, PTPRF, SLC19A1, SLC39A6, SLC7A1, SPINT2, SYNGR2, TACSTD1, TACSTD2, TM4SF1, TMED3, TMED9, TSPAN8, YIPF1 | 2.57 |
| Groups 2-3. Ion transporters (including metal ion and ATP dependent transporters) |
14 (35%) | ABCC4, AQP3, ATP2C1, ATP2C2, ATP6V0E2, ATP8A1, CACNA1D, FXYD3, KCNN2, KCNN4, KCNS3, SLC39A6, SLC4A4, TRPV6 | 1.34 - 2.01 |
| II. Gene clusters upregulated in stromal cells (86 clustered genes)c | |||
| Groups 1-3. Organ development and structural proteins (including muscle genes) |
21 (24%) |
COL14A1, COL16A1, COL17A1, COL1A2, COL3A1, COL4A1, COL4A2, COL4A3, COL4A6, COL6A3, SLK ACTC1, ANGPT1, BMP5, CHRDL1, COL4A2, DES, FAM48A, MYH11, MYH6, SCRG1, SERPINF1, TPM1, TPM2 |
5.87 - 7.17 |
| Groups 4-5. Structural and extracellular matrix proteins |
12 (14%) | CALM3 (3 loci, Entrez Gene IDs 801, 805, 808), CETN2, EFEMP1, EFEMP2, FBLN1, MATN2, NELL2, NID2, PLS3, S100A4 | 4.14 - 4.87 |
| Group 6-7, 10. immune and inflammation related proteins |
22 (26%) | BTN3A2, BTN3A3, C1S, C3, C7, CCR5, CDH10, CFD, CLU, CX3CR1, CXCR4, EDNRA, FZD7, HLA-DPA1, HLA-DQA2, HLA-DQB2, IL6ST, JAM3, LPHN1, MCAM, SERPING1, SGCG | 1.9 - 3.47 |
| Group 8. zinc finger transcription factors |
10 (12%) | CSRP1, CSRP2, DZIP1, FHL1, LDB3, LMO3, MBNL1, MBNL2, PEG3, ZFP36L1 | 2.49 |
| Groups 9, 11. metal ion transporters and regulators |
17 (20%) | ARVC2, ATP1A2, C10ORF56, CHN1, FHM2, FXYD6, ITPR1, KCNAB1, KCNMA1, KIR6.1, MBLL, PDZRN4, SERCA2, SLC24A3, SP140L, STAC, TRPC4 | 1.56 - 2.06 |
a. Classification of 496 genes performed by DAVID Gene Ontology analysis, terms based primarily on GO_BP, GO_MF,GO_CC terms
b. %of total clustered genes in parenthesis
c. 11% of upregulated epithelial and 28% of upregulated stromal genes were clustered into 3 and 11 functional clusters, respectively