Table 1.

Upregulated genes identified by statistical analysis and database interrogation

Gene nameLocationFunctionMethylation
NM_000228_1—LAMB31q32.2Cell communication(40)
NM_005319_1—H1F26p22.2Nucleosome condensationUnmethylated
NM_000598_1—IGFBP37p13Cell growth and differentiation, apoptosis(15)
NM_002353_1—TACSTD21p32.1Receptor activityMethylated (LNCaP)
NM_000852_1—GSTP111q13.2Transferase activity(13)
NM_019554_1—S100A41q21.3Calcium ion binding(41)
NM_006332_1—IFI3019p13.11Immune responseMethylated (LNCaP, PC-3)
NM_004165_1—RRAD16q22.1Nucleotide binding, GTPase activity(42)
NM_000574_1—DAF1q32.2Complement activationUnmethylated
XM_027365_1—ARL6IP16p12.3Protein transport, cell signalingUnmethylated
NM_001647_1—APOD3q29Lipid metabolic process(31)
NM_014164_1—FXYD519q13.12Cell adhesionUnmethylated
NM_002306_1—LGALS314q22.3Extracellular matrix organization, biogenesis(43)
NM_001924_1—GADD45a1p31.2Apoptosis, DNA repair(31)
NM_001909_1—CTSD11p15.5ProteolysisUnmethylated
NM_005556_1—KRT712q13.13Cytoskeleton organization and biogenesisMethylated (LNCaP, MDA2b)
NM_003246_1—THBS115q14Cell motility and adhesion, inflammation(44)
AF373867_1—TBX1C22q11.21Transcription factorUnmethylated
NM_004039_1—ANXA215q22.2Calcium ion bindingMethylated (LNCaP)
NM_002167_1—ID31p36.12Negative regulation of transcription(31)
NM_002165_1—ID120q11.21Negative regulation of transcriptionUnmethylated
NM_004925_1—AQP39p13.3TransportMethylated (LNCaP)
NM_000610_1—CD4411p13Cell adhesion(45)
NM_003687_1—PDLIM45q23.3Protein, metal ion binding(14)
NM_002084—GPX35q33.1Glutathione peroxidase activity(31)
NM_002229_1—JUNB19p13.13Transcription factor(31)
NM_006005_1—WFS14p16.1Putative transmembrane proteinNot done
NM_001953_1—ECGF122q13.33Growth factorUnmethylated
NM_004417_1—DUSP15q35.1Protein binding(31, 34)
NM_006111_1—ACAA218q21.1Acetyl-CoA c-acyltransferase activityUnmethylated
NM_005822_1—DSCR1L16p12.3Central nervous system developmentNot done
NM_002204_1—ITGA317q21.33ReceptorUnmethylated
NM_006496_1—GNAI317q24.1Nucleotide bindingUnmethylated
NM_006509_1—RELB19q13.32Transcription factorUnmethylated
NM_005536_1—IMPA18q21.13Phosphatidylinositol biosynthetic processNot done
NM_006317_1—BASP15q15.1Brain acid-soluble proteinMethylated in all four lines
AL050044_1—GADD45b (hypothetical protein dkfzp566b133)19p13.3Apoptosis, regulation of MAPKK activityMethylated (DU-145, LNCaP)
NM_005737_1—ARL72q37.1Binds and exchanges GTP and GDPUnmethylated
NM_005919_1—MEF2B19p13.11Transcription factorNot done
NM_001673_1—ASNS7q21.3Aspartate and asparagine activityUnmethylated
NM_005253_1—FOSL22p23.2Transcription factorUnmethylated
NM_016582_1—SLC15A3 (PHT2)11q12.2Transporter activityMethylated in all four lines
NM_021967_1—SERF1A5q13.2Nervous system developmentNot done
NM_001386_1—DPYSL28p21.2Dihydropyrimidinase activityNot done
NM_002083_1—GPX214q23.3Response to oxidative stressNot done

NOTE: The table shows 45 genes that showed at least 2-fold upregulation in at least one of the four cell lines. Gene names in bold indicate genes identified as hypermethylated in prostate cancer cells in this study. Gene names in bold italics indicate genes previously identified as under epigenetic regulation in prostate cancer cells. Location is chromosomal map location. The tumor cell lines identified as hypermethylated by bisulfite sequencing are listed. Numbered references indicate published report of DNA methylation or other epigenetic regulation. Gene function was obtained from Entrez Gene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene).

Abbreviation: MAPKK, mitogen-activated protein kinase kinase.