Table 2.

SAM-identified CGI genes hypermethylated in group 2 tumors relative to group 1 tumors

CGI clone IDChromosome locationGeneGenbank
FR#1-B51q23.3LMX1ANM_177398
FR#4-G9*1q32.3RAMPAF195765
FR#1-B82p23.1LBHAF110224
CG2:45-B052q31.3NEUROD1D82347
CpG10-B32q33.1MetRSAB107013
CG2:17-F09*3p14.1BAIAP1AB010894
CG2:34-G01*3q25SHOX2AF022654
CG2:41-B033p25.3VGLL4D50911
FR#2-E12*4q21.2NKX6-1NM_006168
CG2:30-A075p15.2CCT5BC035499
FJ#13-A55q33.1ATOX1NM_004045
FR#4-H2*6p21.33PRR3U63336
FR#2-G2*6p22.1HIST1H2BJNM_021058
FJ#45-F26q13DDX43AJ278110
CG2:18-A03*6q16.3SIM1HM_005068
FR#3-H17q21.2CDK6NM_001259
CG2:40-A107q33CNOT4BC035590
CG2:36-F128p22DLC1AB051510
FJ#38-E510p13PRPF18BC002572
FJ#39-H9*10q26.13FAM53BNM_014661
FR#2-G12*11p13BDNFAY054400
FJ#38-F112q13.13CBX5BC006821
CG2:20-A0612q22METAP2U29607
CG2:34-H1215q22.2NLF2AW292865
FJ#26-B115q25.1DNAJA4AK098079
FJ#17-H615q14AQRAB011132
FJ#27-B316p11.2SPINLNM_032038
CG2:29-H03*16p13.3ADCY9AB011092
FJ#19-C7*16p13.3CCNFNM_001761
FR#3-E416q23.1WWOXAF211943
FR#5-E817q11.2SPAG5AF399910
CG2:43-H0517p13.1PIK3R5AF128881
FR#6-C1*19p13.11FKBP8NM_012181
CG2:20-B0119p13.3BSGAY358113
FJ#20-F11*19q13.32OPA3AK098798
CG2:38-G07*19q13.4PRKCGBC047876
FJ#13-G519q13.43UBE2sBC004236
CpG14-C820q11.23NDRG3AB044943
FR#1-F7*22q13.31CERKNM_182661
FJ#26-D12*Xq24PGRMC1NM_006667
  • NOTE: Identified genes were within 2 kb span of CGI sequence match to the genome. Additional list of CGI genes and loci is presented in Supplementary Table S1.

  • * CGI loci screened on the validation array.