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Table 3 Top 20 ranked candidate CpG probes and associated genes

From: Random forest-based modelling to detect biomarkers for prostate cancer progression

CG probe names Chr. Location Mean decrease in accuracy Mean decrease in Gini ChromHMM PC3 ChromHMM PrEC ChromHMM LNCaP Gene symbol Distance from TSS (bp) Mean meth. good progn. Mean meth. poor progn.
cg07443748 chr22 17073594 0.002194 0.221948 Heterochromatin Heterochromatin Heterochromatin CCT8L2 105 0.585 0.434
cg18146506 chr20 2633340 0.002382 0.193534 Promoter Promoter Promoter NOP56 550 0.430 0.327
cg05766896 chr1 157789933 0.001993 0.192736 Heterochromatin Heterochromatin Heterochromatin FCRL1 − 39 0.657 0.508
cg16734913 chr11 55681277 0.001621 0.167347 Heterochromatin Heterochromatin Heterochromatin OR5W2 780 0.688 0.567
cg16876647 chr2 43451842 0.002281 0.15899 Promoter Promoter Heterochromatin ZFP36L2 1905 0.703 0.401
cg24100636 chr12 3600087 0.001015 0.145156 Heterochromatin Promoter Heterochromatin PRMT8 −  314 0.280 0.446
cg16377872 chr19 15084823 0.00141 0.143848 Heterochromatin Heterochromatin Heterochromatin SLC1A6 − 1094 0.747 0.641
cg27212232 chr20 53091600 0.001276 0.143601 Heterochromatin Heterochromatin Heterochromatin DOK5 − 535 0.407 0.301
cg02601618 chr22 17075046 0.002015 0.134821 Heterochromatin Heterochromatin Heterochromatin CCT8L2 − 1347 0.696 0.565
cg12092201 chr2 43451775 0.001586 0.122542 Promoter Promoter Heterochromatin ZFP36L2 1972 0.473 0.285
cg12818557 chr8 89340139 0.00084 0.122408 Heterochromatin Promoter Promoter MMP16 − 423 0.329 0.503
cg04211581 chr6 152011656 0.000859 0.117083 CTCF Heterochromatin Transcribed ESR1 26 0.458 0.317
cg24690071 chr13 100635352 0.001171 0.116259 Poised promoter Repressed Promoter ZIC2 1327 0.483 0.322
cg00874055 chr1 236306673 0.001063 0.115871 Promoter Promoter Poised promoter GPR137B 842 0.487 0.342
cg10562114 chr10 120790501 0.000745 0.112334 Promoter Promoter Promoter NANOS1 1274 0.353 0.230
cg26135325 chr1 152595322 0.000427 0.104978 Heterochromatin Heterochromatin Heterochromatin LCE3A 256 0.540 0.431
cg00343414 chr11 109292465 0.000626 0.10478 Heterochromatin Heterochromatin Heterochromatin C11orf87 − 380 0.795 0.691
cg25458871 chr19 57352584 0.000731 0.104688 Heterochromatin Heterochromatin Heterochromatin PEG3 − 521 0.532 0.428
cg25458871 chr19 57352584 0.000731 0.104688 Heterochromatin Heterochromatin Heterochromatin ZIM2 − 488 0.532 0.428
cg16118839 chr11 88069169 0.000997 0.103679 Promoter Enhancer Heterochromatin CTSC 1785 0.526 0.408
cg16776350 chr1 160549158 0.000666 0.102419 Heterochromatin Heterochromatin Heterochromatin CD84 135 0.590 0.459
cg00636390 chr8 57027352 0.000914 0.101489 Heterochromatin Repressed Repressed MOS − 812 0.616 0.485
cg17225407 chr17 41176954 0.000767 0.101076 Poised promoter Poised promoter Heterochromatin RND2 − 303 0.388 0.287