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. 2016 Sep 27;6:33435. doi: 10.1038/srep33435

Table 3. Validation of the direction of methylation comparing lymph node metastasis (LN) to matched normal adjacent tissue (NAT).

Gene name LNvNAT
450K array
 MBDcap seq
 Gene expression
p-value Methylation difference Mapinfo ENHANCER(E)/PROMOTER(P) UCSC_REFGENE_GROUP p-value Fold change Region Fold change p-value
GREB1 0.007 −0.207 11673928 TSS1500 0.045 −2.329 Chr2: 11722242-11723241 −1.57 0.000129  
0.015 −0.160 11674057 TSS200  
0.008 −0.180 11674557 5′UTR  
0.048 −0.234 11724901 gene body  
0.005 −0.173 11734257 gene body  
0.040 −0.132 11761803 gene body  
RBMS3 0.003 −0.176 29782270 E gene body 0.032 −2.538 chr3: 29345803-29346802 −2.3 1.10E-05
0.049 −2.270 chr3: 29404803-29405802
0.009 −3.316 chr3: 29434803-29435802
0.010 −3.257 chr3: 29481803-29482802
0.049 −2.277 chr3: 29488803-29489802
0.009 −3.290 chr3: 29498803-29499802
0.010 −3.263 chr3: 29516803-29517802
0.040 −2.393 chr3: 29630803-29631802
0.021 −2.795 chr3: 29636803-29637802
0.040 −2.393 chr3: 29665803-29666802
0.011 −3.191 chr3: 29748803-29749802
0.021 −2.796 chr3: 29843803-29844802
0.040 −2.393 chr3: 29871803-29872802
0.003 −4.143 chr3: 29921803-29922802
0.005 −3.667 chr3: 29962803-29963802
MME 0.023 −0.104 154900894   3′UTR 0.001 −5.259 chr3: 154794913-154795912 −3.06 3.65E-07
PLSCR4 0.000 0.141 145968692   5′UTR 0.007 3.496 chr3: 145941967-145942966 −2.3 1.10E-05
IGSF10 0.001 −0.101 151176684   TSS200 0.041 −2.379 chr3: 151172498-151173497 −2.26 4.52E-05
APOD 0.017 −0.135 195299575 E gene body 0.011 −3.205 chr3: 195296077-195297076 −9.46 2.33E-0.6
LIFR 0.008 −0.140 38535574 E 5′UTR 0.048 −2.284 chr5: 38484508-38485507 −2.43 5.93E-05
0.025 −2.678 chr5: 38522508-38523507
0.040 −2.393 chr5: 38524508-38525507
0.014 −0.284 38595383 1st Exon 5′UTR 0.020 −2.813 chr5: 38562508-38563507  
0.045 −2.323 chr5: 38575508-38576507          
IL20RA 0.002 −0.193 137362747   gene body 0.025 −2.697 chr6: 137323299-137324298 −1.7 1.49E-05
0.008 −3.424 chr6: 137348299-137349298
CD36 0.029 −0.193 80252533 E 5′UTR 0.040 −2.393 chr7: 80009891-80010890 −2.57 2.77E-06
0.032 −0.137 80274687   TSS1500 0.040 −2.393 chr7: 80254891-80255890
0.040 −2.393 chr7: 80285891-80286890
LRRC17 0.004 0.150 102574445 E gene body 0.047 2.303 chr7: 102561344-102562343 −1.67 6.38E-05
0.012 0.112 102574475 E gene body
0.037 0.110 102574504 E gene body
0.039 0.169 102583144   gene body
AGR3 0.000 −0.139 16922492   TSS1500 0.025 −2.697 chr7: 16898614-16899613 −2.87 1.44E-08
RELN 0.010 −0.148 103279088 E gene body 0.013 −3.083 chr7: 103216964-103217963 −1.8 0.000112
0.040 −2.393 chr7: 103220964-103221963
0.040 −2.393 chr7: 103250964-103251963
0.008 −3.403 chr7: 103261964-103262963
0.039 −0.213 103301932 E gene body 0.037 −2.449 chr7:103348964-103349963
0.006 −3.547 chr7:103404964-103405963
0.029 −2.595 chr7:103449964-103450963
0.034 −2.495 chr7:103450964-103451963
0.037 −2.451 chr7:103566964-103567963
CDCA2 0.017 −0.204 25317638   5′UTR 0.044 −2.345 chr8:25320513-25321512 1.9 0.000302
0.005 −3.704 chr8:25321513-25322512
0.006 −3.610 chr8:25325513-25326512
MMP16 0.049 −0.144 89053427 E 3′UTR 0.010 −3.247 chr8:89313718-89314717 −1.57 9.02E-05
0.027 −0.222 890966
0.041 −0.101 89218697 E gene body
0.036 −0.113 89231006 E gene body
0.042 −0.198 89241632 E gene body
0.039 −0.194 89255591 E gene body
SVEP1 0.005 0.243 113308063 E gene body 0.005 −3.650 chr9:113134161-113135160 −1.87 1.43E-05
0.001 −4.528 chr9:113173161-113174160
0.001 4.632 chr9:113179161-113180160
0.033 −2.510 chr9:113201161-113202160
0.008 −0.122 113316190 E gene body 0.012 −3.147 chr9:113228161-113229160
0.020 2.810 chr9:113266161−113267160
0.005 −3.681 chr9:113268161-113269160
0.001 −5.016 chr9:113324161-113325160
ITIH5 0.045 −0.147 7614151   gene body 0.032 −2.539 chr10:7628962-7629961 −1.78 3.16E-05
0.000 −0.241 7614570   gene body 0.029 −2.592 chr10:7644962-7645961
0.042 −0.171 7617637   gene body 0.025 −2.680 chr10:7646962-7647961
0.048 −0.142 7618474   gene body 0.045 −2.329 chr10:7649962-7650961
0.028 −0.174 76514031 E gene body 0.031 −2.548 chr10:7662962-7663961
0.022 −0.101 7661622   TSS200 0.001 −4.689 chr10:7699962-7700961
0.027 −0.115 7662761   TSS1500      
MEG3 0.003 −0.120 101291100   TSS1500 0.005 −3.724 chr14:101318445-101319444 −2.8 1.79E-08
0.033 −0.201 101296297   gene body 0.026 −2.672 chr14:101319445-101320444
0.020 −0.223 101317622   TSS1500      
TSHZ2 0.019 0.239 51592177   gene body 0.048 −2.287 chr20:51601946-51602945 −2.33 3.94E-05
0.005 −3.707 chr20:51684946-51685945
0.001 −4.547 chr20:51752946-51753945
0.000 −6.638 chr20:51790946-51791945
0.038 −2.422 chr20:51819946-51820945
0.047 −0.190 52029943   3′UTR 0.041 −2.386 chr20:51825946-51826945
0.035 −2.488 chr20:51879946-51880945
0.026 −2.672 chr20:51914946-51915945
0.043 −2.353 chr20:51928946-51929945
0.037 2.453 chr20:51956946-51957945
0.041 −01.19 52036204   3′UTR 0.021 −2.803 chr20:51995946-51996945
0.036 −2.457 chr20:52006946-52007945
0.050 −2.268 chr20:52049946-52050945
0.016 2.954 chr20:52082946-52083945
0.046 −2.311 chr20:52103946-52104945

Genes in the first column were identified to be associated with LM in our previous study. Using the 450K methylation arrays we identified single loci within these genes to be differentially methylated comparing LN versus NAT samples (mapinfo shows location of the significant loci). The Methylation-Binding-Domain-Capture sequencing (MBDcap seq) provides regional methylation analysis. The analysed regions start 2kb upstream from the first transcription start side to the end of the gene in 1kb tiles.