. 2012 Mar;180(3):895–903. doi: 10.1016/j.ajpath.2011.11.030

Table 1.

Genes Affected by Copy Number and Expression Alterations

Up-regulated and amplified genes (n = 34)	Down-regulated and deleted genes (n = 198)
AR, ASNS, BOP1, C20orf20, CANT1, CCDC78, CELSR3, CLDN3, DOCK4, DVL1, EDA, EEF1D, EPPK1, EZH2, FABP5, FASN, FBXL6, HIP1, HLTF, KSR2, LRRC14, ORAI2, PDIA2, PHF8, PRKAG2, PRKAR2A, PTK6, PYCRL, RHPN1, SLC26A6, STMN2, WDSOF1, ZNF707, ZP3	ABHD13, ACTA2, ADAD2, ADAM32, ADAM7, ADAMDEC1, ADAMTS18, ADRA1A, ADRB3, AJ291678, AJ412029, AK056689, AK098579, ANKRD11, ARHGEF15, ATP9B, BC043547, BCMO1, BLK, BRUNOL4, C10orf59, C13orf1, C13orf18, C6orf159, C6orf165, CCBE1, CD180, CDADC1, CES7, CLN5, CNDP1, CNR1, CNTNAP4, COMMD6, CSNK1A1L, CYBA, CYP2C9, DAOA, DCT, DCTN6, DEFA4, DEFA5, DEFA6, DEFB1, DEFB4, DGKH, DHRS12, DLEU7, DLGAP2, DYNLRB2, EBF2, EDNRB, EGR3, ELF1, EPHX2, EPSTI1, EXOC6, EXTL3, FAM124A, FAM3B, FGF17, FGF20, FGL1, FHOD3, FLJ22167, FLJ37543, FUT10, FUT9, GABARAPL2, GABRR1, GALR1, GFRA2, GLP2R, GNAO1, GOT2, GPR63, GRIK2, HDDC2, HPSE2, HS3ST3A1, HS3ST3B1, HS3ST5, HTR1A, HTR1E, IFIT2, IGSF5, ITM2B, KCNG4, KCTD9, KIAA0513, KIAA1704, KIF13B, KLF5, KLHL32, LDB3, LDHD, LETM2, LGI3, LIX1, LPCAT2, LRIT1, LRP1B, MAF, MAP1LC3B, MC4R, MCHR2, ME1, MFHAS1, MIER3, MLNR, MX1, MYO16, MYOCD, NAT1, NAT2, NDFIP2, NEFL, NEFM, NETO1, NKAIN2, NRG1, NT5E, NTN1, NUDT15, NUDT7, ODF4, OLFM4, OPN4, OR4K1, PABPC4L, PCDH10, PCDH8, PCDH9, PCP4, PDLIM2, PEBP4, PIBF1, PIK3C2G, PIK3R6, PIWIL2, PKD1L2, PLEKHA2, PLEKHA5, PMFBP1, PNMA2, PNOC, PPAPDC1B, PPP1R3C, PPP2CB, PRDM13, PRDM7, PTCD2, PTEN, RAD17, RAX, RCBTB2, RIOK2, RTTN, SCARA5, SCEL, SEC63, SERP2, SERPINB11, SERPINB13, SERPINB3, SERPINB5, SERPINB7, SFTPC, SH3BGR, SLC16A12, SLC18A1, SLC35A1, SLC6A2, SMAD9, SOHLH2, SOX7, SPACA1, SPG20, STAR, STMN4, SUCLA2, TAT, THSD7B, TMEM174, TMEM66, TNFRSF10C, TNFRSF10D, TNKS, TRIM23, TUSC3, UNC5D, WBP4, WDR16, WISP3, ZC3H13, ZDHHC2, ZFP1, ZNF516

Up-regulated and amplified genes (n = 34)

Down-regulated and deleted genes (n = 198)

AR, ASNS, BOP1, C20orf20, CANT1, CCDC78, CELSR3, CLDN3, DOCK4, DVL1, EDA, EEF1D, EPPK1, EZH2, FABP5, FASN, FBXL6, HIP1, HLTF, KSR2, LRRC14, ORAI2, PDIA2, PHF8, PRKAG2, PRKAR2A, PTK6, PYCRL, RHPN1, SLC26A6, STMN2, WDSOF1, ZNF707, ZP3

ABHD13, ACTA2, ADAD2, ADAM32, ADAM7, ADAMDEC1, ADAMTS18, ADRA1A, ADRB3, AJ291678, AJ412029, AK056689, AK098579, ANKRD11, ARHGEF15, ATP9B, BC043547, BCMO1, BLK, BRUNOL4, C10orf59, C13orf1, C13orf18, C6orf159, C6orf165, CCBE1, CD180, CDADC1, CES7, CLN5, CNDP1, CNR1, CNTNAP4, COMMD6, CSNK1A1L, CYBA, CYP2C9, DAOA, DCT, DCTN6, DEFA4, DEFA5, DEFA6, DEFB1, DEFB4, DGKH, DHRS12, DLEU7, DLGAP2, DYNLRB2, EBF2, EDNRB, EGR3, ELF1, EPHX2, EPSTI1, EXOC6, EXTL3, FAM124A, FAM3B, FGF17, FGF20, FGL1, FHOD3, FLJ22167, FLJ37543, FUT10, FUT9, GABARAPL2, GABRR1, GALR1, GFRA2, GLP2R, GNAO1, GOT2, GPR63, GRIK2, HDDC2, HPSE2, HS3ST3A1, HS3ST3B1, HS3ST5, HTR1A, HTR1E, IFIT2, IGSF5, ITM2B, KCNG4, KCTD9, KIAA0513, KIAA1704, KIF13B, KLF5, KLHL32, LDB3, LDHD, LETM2, LGI3, LIX1, LPCAT2, LRIT1, LRP1B, MAF, MAP1LC3B, MC4R, MCHR2, ME1, MFHAS1, MIER3, MLNR, MX1, MYO16, MYOCD, NAT1, NAT2, NDFIP2, NEFL, NEFM, NETO1, NKAIN2, NRG1, NT5E, NTN1, NUDT15, NUDT7, ODF4, OLFM4, OPN4, OR4K1, PABPC4L, PCDH10, PCDH8, PCDH9, PCP4, PDLIM2, PEBP4, PIBF1, PIK3C2G, PIK3R6, PIWIL2, PKD1L2, PLEKHA2, PLEKHA5, PMFBP1, PNMA2, PNOC, PPAPDC1B, PPP1R3C, PPP2CB, PRDM13, PRDM7, PTCD2, PTEN, RAD17, RAX, RCBTB2, RIOK2, RTTN, SCARA5, SCEL, SEC63, SERP2, SERPINB11, SERPINB13, SERPINB3, SERPINB5, SERPINB7, SFTPC, SH3BGR, SLC16A12, SLC18A1, SLC35A1, SLC6A2, SMAD9, SOHLH2, SOX7, SPACA1, SPG20, STAR, STMN4, SUCLA2, TAT, THSD7B, TMEM174, TMEM66, TNFRSF10C, TNFRSF10D, TNKS, TRIM23, TUSC3, UNC5D, WBP4, WDR16, WISP3, ZC3H13, ZDHHC2, ZFP1, ZNF516