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

Gregg et al. BMC Cancer 2010 10:165   doi:10.1186/1471-2407-10-165

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