Table 3. Putative deleted genes and their expression in the LNCaP and PC3 prostate cancer cell lines.
| Symbol | Description | CNV Region | Gene Start | Gene End | NP UPC | LNCaP UPC | PC3 UPC |
|---|---|---|---|---|---|---|---|
| LNCaP | |||||||
| PWRN1 | Prader-Willi region nonprotein coding RNA 1 | 15:24430001–24520000 | 24493137 | 24652130 | 0.0 | 0.0 | 0.0 |
| PC3 | |||||||
| ATP6V0A1 | ATPase H+ transporting V0 subunit a1 | 17:42110001–42520000 | 42458844 | 42522611 | 1 | 1 | 0 |
| CDH18 | Cadherin 18 | 5:19850001–19960000 | 19472951 | 20575873 | 0 | 0 | 0 |
| CIC | Capicua transcriptional repressor | 19:42280001–42320000 | 42268537 | 42295797 | 1 | 1 | 0 |
| CTNNA1 | Catenin α 1 | 5:138770001–138980000 | 138610967 | 138935034 | 1 | 1 | 0 |
| DDX3Y | DEAD-box helicase 3, Y-linked | Y:11530001–16450000 | 12904108 | 12920478 | 1 | 1 | 0 |
| DHX58 | DExH-box helicase 58 | 17:42110001–42520000 | 42101404 | 42112733 | 1 | 0 | 0 |
| DYDC1 | DPY30 domain containing 1 | 10:80250001–80560000 | 80336105 | 80356755 | 0 | 0 | 0 |
| DYDC2 | DPY30 domain containing 2 | 10:80250001–80560000 | 80344745 | 80368073 | 0 | 0 | 0 |
| FAM213A | Family with sequence similarity 213 member A | 10:80250001–80560000 | 80407829 | 80437115 | 1 | 0 | 0 |
| GHDC | GH3 domain containing | 17:42110001–42520000 | 42188799 | 42194532 | 1 | 1 | 0 |
| HCRT | Hypocretin neuropeptide precursor | 17:42110001–42520000 | 42184060 | 42185452 | 0 | 0 | 0 |
| HSPB9 | Heat shock protein family B (small) member 9 | 17:42110001–42520000 | 42121431 | 42123352 | 0 | 0 | 0 |
| KAT2A | Lysine acetyltransferase 2A | 17:42110001–42520000 | 42113108 | 42121358 | 1 | 1 | 0 |
| KCNH4 | Potassium voltage-gated channel Subfamily H member 4 | 17:42110001–42520000 | 42156891 | 42181278 | 0 | 0 | 0 |
| LIPJ | Lipase family member J | 10:87910001–88750000 | 88586753 | 88606976 | 0 | 0 | 0 |
| LRRTM2 | Leucine rich repeat transmembrane neuronal 2 | 5:138770001–138980000 | 138868923 | 138875368 | 0 | 0 | 0 |
| MAT1A | Methionine adenosyltransferase 1A | 10:80250001–80560000 | 80271820 | 80289684 | 0 | 0 | 0 |
| MIR548AT | MicroRNA 548at | 17:42110001–42520000 | 42494773 | 42494830 | 0 | 0 | 0 |
| NLGN4Y | Neuroligin 4, Y-linked | Y:11530001–16450000 | 14522638 | 14845650 | 1 | 0.2 | 0 |
| PAFAH1B3 | Platelet activating factor acetylhydrolase 1b catalytic subunit 3 | 19:42280001–42320000 | 42297033 | 42303546 | 1 | 0.7 | 0 |
| PRR19 | Proline rich 19 | 19:42280001–42320000 | 42302098 | 42310821 | 0 | 0 | 0 |
| PTEN | Phosphatase and tensin homolog | 10:87910001–88750000 | 87863113 | 87971930 | 1 | 1 | 0 |
| PTRF | Polymerase I and transcript release factor | 17:42110001–42520000 | 42402452 | 42423517 | 1 | 0 | 0 |
| RAB5C | RAB5C, member RAS oncogene family | 17:42110001–42520000 | 42124976 | 42155044 | 1 | 1 | 0 |
| RNLS | Renalase, FAD dependent amine oxidase | 10:87910001–88750000 | 88273864 | 88584530 | 0.6 | 0 | 0 |
| SH2D4B | SH2 domain containing 4B | 10:80250001–80560000 | 80537902 | 80646560 | 0 | 0 | 0 |
| SIL1 | SIL1 nucleotide exchange factor | 5:138770001–138980000 | 138946720 | 139293557 | 1 | 1 | 0 |
| SIRPB1 | Signal regulatory protein β 1 | 20:1580001–1620000 | 1563521 | 1620061 | 0 | 0 | 0 |
| STAT3 | Signal transducer and activator of transcription 3 | 17:42110001–42520000 | 42313324 | 42388568 | 1 | 1 | 0 |
| STAT5A | Signal transducer and activator of transcription 5A | 17:42110001–42520000 | 42287547 | 42311943 | 1 | 0 | 0 |
| STAT5B | Signal transducer and activator of transcription 5B | 17:42110001–42520000 | 42199168 | 42276707 | 1 | 1 | 0 |
| MEM145 | Transmembrane protein 145 | 19:42280001–42320000 | 42313325 | 42325062 | 0 | 0 | 0 |
| TMSB4Y | Thymosin β 4, Y-linked | Y:11530001–16450000 | 13703567 | 13706024 | 0 | 0 | 0 |
| TSPAN14 | Tetraspanin 14 | 10:80250001–80560000 | 80454166 | 80533123 | 1 | 1 | 0 |
| TSPY1 | Testis-specific protein, Y-linked 1 | Y:9450001–10200000 | 9466955 | 9490081 | 0 | 0 | 0 |
| TTTY13 | Testis-specific transcript, Y-linked 13 (nonprotein coding) | Y:21420001–21630000 | 21583600 | 21594666 | 0 | 0 | 0 |
| TTTY15 | Testis-specific transcript, Y-linked 15 (nonprotein coding) | Y:11530001–16450000 | 12662334 | 12692233 | 1 | 1 | 0 |
| USP9Y | Ubiquitin specific peptidase 9, Y-linked | Y:11530001–16450000 | 12701231 | 12860839 | 1 | 1 | 0 |
| UTY | Ubiquitously transcribed tetratricopeptide repeat containing, Y-linked | Y:11530001–16450000 | 13248379 | 13480673 | 1 | 1 | 0 |
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.