Skip to main content

Table 3 Selected set of 47 potential DNA methylation biomarkers

From: Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

ID CHR Position (hg19) Gene symbol (gene) Methylation Caner_vs_Control LogFC Expression Cancer_vs_Control logFC Correlation Enriched TFa Master-regulatorb
cg02612618 19 22,018,605 ZNF43 0.296 −0.711 −0.743 +  
cg07945582 7 26,206,579 NFE2L3 −0.534 2.858 −0.518 +  
cg00163372 8 128,752,988 MYC −0.682 2.442 −0.498 + +
cg02915837 12 3,069,243 TEAD4 −0.306 2.335 −0.453 +  
cg02334660 4 75,312,483 AREG −0.644 1.711 −0.438   +
cg09386682 3 10,207,069 IRAK2 −0.444 1.614 −0.419   +
cg06972019 1 8,937,448 ENO1 −0.653 1.148 −0.405   +
cg01777575 20 22,566,140 FOXA2 −0.332 1.312 −0.307 +  
cg19377250 7 100,463,206 TRIP6 −0.712 1.356 −0.292   +
cg01952234 11 32,457,130 WT1 0.346 1.004 −0.227   +
cg05931439 14 23,305,957 MMP14 −0.486 1.439 −0.212   +
cg20063095 2 134,977,141 MGAT5 −0.459 1.162 −0.209   +
cg17726575 2 11,606,945 E2F6 −0.420 1.259 −0.204 +  
cg18696576 6 34,203,630 HMGA1 −0.328 1.758 −0.190 +  
cg06899755 1 218,520,325 TGFB2 0.296 0.946 −0.171   +
cg01742897 18 53,257,019 TCF4 0.184 0.021 −0.166 +  
cg15555970 18 3,452,317 TGIF1 −0.294 1.511 −0.161 +  
cg00419314 4 74,735,092 CXCL1 −0.313 3.903 −0.145   +
cg11924517 6 52,050,597 IL17A −0.747 0.889 −0.145   +
cg18618815 17 48,275,324 COL1A1 −0.428 2.085 −0.142   +
cg08460026 2 204,732,474 CTLA4 −0.699 1.022 −0.110   +
cg00425708 12 66,217,779 HMGA2 −0.284 1.016 −0.105 +  
cg08018731 7 150,687,961 NOS3 −0.631 1.958 −0.059   +
cg01813071 11 102,401,616 MMP7 −0.367 4.814 −0.055   +
cg02425416 11 2,163,808 IGF2 −0.419 1.353 −0.025   +
cg13635007 8 29,210,154 DUSP4 −0.408 2.309 −0.018   +
cg07330438 21 37,258,460 RUNX1 −0.556 1.525 −0.011 +  
cg06547715 2 218,990,976 CXCR2 −0.570 1.036 0.005   +
cg08836542 2 28,618,831 FOSL2 −0.386 −0.027 0.006 +  
cg02059626 8 76,319,264 HNF4G −0.365 −0.209 0.026 +  
cg04567009 1 161,600,769 FCGR3B −0.573 1.727 0.048   +
cg01421342 11 14,995,754 CALCA 0.309 1.043 0.052   +
cg26367719 19 55,875,605 IL11 −0.568 2.039 0.082   +
cg01830294 7 116,963,492 WNT2 0.132 2.494 0.128   +
cg01664670 20 39,316,308 MAFB 0.280 −0.226 0.140 +  
cg01824511 14 38,064,456 FOXA1 −0.430 −0.768 0.141 +  
cg00697440 3 121,795,768 CD86 −0.584 0.105 0.141   +
cg01589587 14 76,002,440 BATF −0.416 1.028 0.222 +  
cg24093411 5 133,449,651 TCF7 0.387 2.022 0.321 +  
cg02991571 13 28,501,126 PDX1 0.541 2.869 0.353 +  
cg06613263 5 142,779,552 NR3C1 −0.588 −0.931 0.410 +  
cg03130910 1 234,908,226 BMP3 −1.107 −2.482 0.601   
cg05259836 6 74,290,516 PYY −0.813 −5.604 0.601   
cg24032190 15 67,442,893 ADH1B −1.071 −3.781 0.603   
cg04786142 1 234,908,381 NR5A2 −1.075 −1.644 0.606   
cg03800922 6 74,290,220 CA1 −0.842 −6.934 0.610   
cg26541218 7 47,826,387 KLF4 −0.771 −1.938 0.617   
  1. aThe column “Enriched TF” marks genes that encode TFs whose sites found enriched around CpG loci
  2. bThe column “Master regulator” marks genes that encode master-regulator molecules identified in the study