Table 3 Putative deleted genes and their expression in the LNCaP and PC3 prostate cancer cell lines
SymbolDescriptionCNV RegionGene StartGene EndNP UPCLNCaP UPCPC3 UPC
LNCaP
 PWRN1Prader-Willi region nonprotein coding RNA 115:24430001–2452000024493137246521300.00.00.0
PC3
 ATP6V0A1ATPase H+ transporting V0 subunit a117:42110001–425200004245884442522611110
 CDH18Cadherin 185:19850001–199600001947295120575873000
 CICCapicua transcriptional repressor19:42280001–423200004226853742295797110
 CTNNA1Catenin α 15:138770001–138980000138610967138935034110
 DDX3YDEAD-box helicase 3, Y-linkedY:11530001–164500001290410812920478110
 DHX58DExH-box helicase 5817:42110001–425200004210140442112733100
 DYDC1DPY30 domain containing 110:80250001–805600008033610580356755000
 DYDC2DPY30 domain containing 210:80250001–805600008034474580368073000
 FAM213AFamily with sequence similarity 213 member A10:80250001–805600008040782980437115100
 GHDCGH3 domain containing17:42110001–425200004218879942194532110
 HCRTHypocretin neuropeptide precursor17:42110001–425200004218406042185452000
 HSPB9Heat shock protein family B (small) member 917:42110001–425200004212143142123352000
 KAT2ALysine acetyltransferase 2A17:42110001–425200004211310842121358110
 KCNH4Potassium voltage-gated channel Subfamily H member 417:42110001–425200004215689142181278000
 LIPJLipase family member J10:87910001–887500008858675388606976000
 LRRTM2Leucine rich repeat transmembrane neuronal 25:138770001–138980000138868923138875368000
 MAT1AMethionine adenosyltransferase 1A10:80250001–805600008027182080289684000
 MIR548ATMicroRNA 548at17:42110001–425200004249477342494830000
 NLGN4YNeuroligin 4, Y-linkedY:11530001–16450000145226381484565010.20
 PAFAH1B3Platelet activating factor acetylhydrolase 1b catalytic subunit 319:42280001–42320000422970334230354610.70
 PRR19Proline rich 1919:42280001–423200004230209842310821000
 PTENPhosphatase and tensin homolog10:87910001–887500008786311387971930110
 PTRFPolymerase I and transcript release factor17:42110001–425200004240245242423517100
 RAB5CRAB5C, member RAS oncogene family17:42110001–425200004212497642155044110
 RNLSRenalase, FAD dependent amine oxidase10:87910001–8875000088273864885845300.600
 SH2D4BSH2 domain containing 4B10:80250001–805600008053790280646560000
 SIL1SIL1 nucleotide exchange factor5:138770001–138980000138946720139293557110
 SIRPB1Signal regulatory protein β 120:1580001–162000015635211620061000
 STAT3Signal transducer and activator of transcription 317:42110001–425200004231332442388568110
 STAT5ASignal transducer and activator of transcription 5A17:42110001–425200004228754742311943100
 STAT5BSignal transducer and activator of transcription 5B17:42110001–425200004219916842276707110
 MEM145Transmembrane protein 14519:42280001–423200004231332542325062000
 TMSB4YThymosin β 4, Y-linkedY:11530001–164500001370356713706024000
 TSPAN14Tetraspanin 1410:80250001–805600008045416680533123110
 TSPY1Testis-specific protein, Y-linked 1Y:9450001–1020000094669559490081000
 TTTY13Testis-specific transcript, Y-linked 13 (nonprotein coding)Y:21420001–216300002158360021594666000
 TTTY15Testis-specific transcript, Y-linked 15 (nonprotein coding)Y:11530001–164500001266233412692233110
 USP9YUbiquitin specific peptidase 9, Y-linkedY:11530001–164500001270123112860839110
 UTYUbiquitously transcribed tetratricopeptide repeat containing, Y-linkedY:11530001–164500001324837913480673110
  • CNV regions are listed for putative homozygous deletion events (CNV = 0). UPC refers to Universal exPression Code score, where UPC value > 0.5 indicates that a gene is actively transcribed. CNV, copy number variation; NP, normal prostate tissue; RAB5C, Ras-related protein Rab-5C; FAD, flavin adenine dinucleotide.