Table 1.
Gene-related Loci Ranked by Significance.
| Gene | Gene Name | Accession No. | Location | Hypermethylation or Hypomethylation | Distance to TSS | CpG Island | Gene Body | Exon/Intron |
| MCF2L* | Cell line derived transforming sequence-like | NM_024979 | Chr13: 112,704,068–112,792,498 | Hyper | +117331 | Y | Y | Intron |
| RAB11FIP3* | RAB11 family interacting protein 3 | NM_014700 | Chr16: 415,668–512,482 | Hypo | +31178 | Y | Y | Intron |
| CNOT3 | CCR4-NOT transcription complex 3 | BC016474 | Chr19: 59,333,294–59,351,230 | Hyper | +10789 | Y | Y | Exon |
| NCR2* | Natural cytotoxicity triggering receptor 2 | AJ010100 | Chr6: 41,411,566–41,426,579 | Hypo | +14989 | Y | Y | Exon |
| IER5L | Immediate early response 5-like | NM_203434 | Chr9: 130,978,873–131,012,683 | Hypo | -28327 | N | N | - |
| SERF2 | Small EDRK-rich factor 2 | BC015491 | Chr15: 41,871,834–41,873,536 | Hyper | +15217 | Y | Y | Exon |
| FRMD5 | FERM domain containing 5 | NM_032892 | Chr15: 41,952,764–42,274,683 | Hypo | +311563 | N | Y | Intron |
| MCF2L | Cell line derived transforming sequence-like | NM_024979 | Chr13: 112,704,068–112,792,498 | Hyper | +65503 | N | Y | Intron |
| FAM83C | Family with sequence similarity 83 C | NM_178468 | Chr20: 33,336,947–33,343,639 | Hyper | +189 | Y | Y | Exon |
| FRMD5 | FERM domain containing 5 | NM_032892 | Chr15: 41,952,764–42,274,683 | Hypo | +321825 | N | N | - |
| DEPDC5 | DEP domain containing 5 | AJ698951 | Chr22: 30,480,852–30,632,599 | Hypo | +151926 | N | Y | Intron |
| EVX1* | Even-skipped homeobox 1 | NM_001989 | Chr7: 27,248,945–27,252,717 | Hyper | +1419 | Y | Y | Intron |
| MAP1A | Microtubule-associated protein 1A | NM_002373 | Chr15: 41,597,132–41,611,110 | Hypo | +4246 | Y | Y | Exon |
| FGF1* | Fibroblast growth factor 1 | NM_000800 | Chr5: 141,953,305–142,045,812 | Hypo | +29175 | Y | Y | Intron |
| SYN3 | Synapsin III | NM_003490 | Chr22: 31,238,539–31,732,683 | Hypo | +284369 | N | Y | Intron |
| GRM8 | Glutamate receptor, metabotropic 8 | NM_000845 | Chr7: 125,865,894–126,670,548 | Hypo | +584116 | N | Y | Intron |
| SERPINB8 | Serpin peptidase inhibitor B8 | BC034528 | Chr18: 59,788,332–59,804,866 | Hyper | +374 | Y | Y | Intron |
| CAV1* | Caveolin 1 | AF 172085 | Chr7: 115,953,642–115,986,904 | Hyper | +1855 | Y | Y | Exon |
| WNT2* | Wingless-type MMTV integration site | BC 078170 | Chr7: 116,704,514–116750565 | Hypo | +19961 | Y | Y | Intron |
| CEP250* | Centrosomal protein | AF022655 | Chr20: 33,511,231–33,563,123 | Hypo | +17863 | N | Y | Intron |
| PI4KCB* | Phosphatidylinositol 4-kinase | NM_002651 | Chr1: 149,531,036–149,565,348 | Hypo | +11021 | N | Y | Intron |
| PISD | Phosphatetidylserine decarboxylase | CR456540 | Chr22: 30,345,379–30,388,195 | Hypo | 13468 | N | N | - |
| GRM8 | Glutamate receptor, metabotropic 8 | NM_000845 | Chr7: 125,865,894–126,670,548 | Hyper | +398576 | N | Y | Intron |
| SPAG4 | Sperm associated antigen 4 | NM_003116 | Chr20: 33,667,222–33,672,379 | Hyper | +1793 | Y | Y | Intron |
| NCR2 | Natural cytotoxicity triggering receptor 2 | AJ010100 | Chr6: 41,411,566–41,426,579 | Hypo | +15264 | Y | N | - |
| FRMD5 | FERM domain containing 5 | NM_032892 | Chr15: 41,952,764–42,274,683 | Hypo | +293027 | Y | Y | Intron |
| NRXN2 | Neurexin 2 | NM_138734 | Chr11: 64,130,221–64,167,363 | Hypo | +81441 | N | Y | Intron |
| ACCN4 | Amiloride-sensitive cation channel 4 | NM_182847 | Chr2: 220,087,295–220,111.738 | Hypo | +3525 | Y | Y | Intron |
| SERPINB2 | Serpin peptidase inhibitor, B2 | NM_002575 | Chr18: 59,705,921–59,722,100 | Hypo | +2820 | N | Y | Intron |
| CEP250 | Centrosomal protein | AF022655 | Chr20: 33,511,231–33,563,123 | Hypo | +18228 | N | Y | Intron |
| FRMD5 | FERM domain containing 5 | NM_032892 | Chr15: 41,952,764–42,274,683 | Hyper | +314296 | N | Y | Intron |
| FER1L4 | Fer-1-like 4 | AL833764 | Chr20: 33,609,920–33,651,008 | Hypo | +46003 | N | Y | Intron |
| ERGIC3 | ERGIC and golgi 3 | AF116614 | Chr20: 33,593,290–33,608,818 | Hypo | +9863 | Y | Y | Intron |
| TRPM8 | Transient receptor potential cation channel | NM_024080 | Chr2: 234,490,781–234,592,905 | Hypo | +8786 | N | Y | Intron |
| TFEB | Transcription factor EB | NM_007162 | Chr6: 41,759,693–41,810,766 | Hypo | +33939 | Y | Y | Intron |
| SEPT8 | Septin | AF440762 | Chr5: 132,114,415–132,140,966 | Hypo | +9050 | Y | Y | Intron |
| EXT1 | Exostoses 1 | BC001174 | Chr8: 118,880,782–119,192,632 | Hypo | +156580 | N | Y | Intron |
| GDF5 | Growth differentiation factor 5 | NM_000557 | Chr20: 33,484,562–33,489,441 | Hypo | +2409 | N | Y | Intron |
| SEPT8 | Septin | AF440762 | Chr5: 132,114,415–132,140,966 | Hypo | +3430 | Y | Y | Intron |
| NRXN2 | Neurexin 2 | NM_138734 | Chr11: 64,130,221–64,167,363 | Hypo | +110421 | Y | Y | Intron |
| TP53BP1 | Tumor protein p53 binding protein 1 | NM_005657 | Chr15: 41,486,698–41,590,028 | Hypo | +15672 | N | Y | Intron |
| F7 | Coagulation factor VII | NM_019616 | Chr13: 112,808,105–112,822,346 | Hypo | +14087 | Y | Y | Exon |
| LILRA5 | Leukocyte immunoglobulin-like receptor A5 | NM_181985 | Chr19: 59,510,164–59,516,221 | Hypo | +2824 | N | Y | Intron |
| DECR2 | 2,4-dienoyl CoA reductase 2 | AK128012 | Chr16: 391,893–402,371 | Hyper | +9490 | Y | Y | Intron |
| FRMD5 | FERM domain containing 5 | NM_032892 | Chr15: 41,952,764–42,274,683 | Hyper | +314576 | N | Y | Intron |
| PI4KCB | Phosphatidylinositol 4-kinase | NM_002651 | Chr1: 149,531,036–149,565,348 | Hypo | +20522 | N | Y | Intron |
| NCR2 | Natural cytotoxicity triggering receptor 2 | AJ010100 | Chr6: 41,411,566–41,426,579 | Hypo | +15109 | Y | N | - |
| MAP1A | Microtubule-associated protein 1A | NM_002373 | Chr15: 41,597,132–41,611,110 | Hypo | +5906 | Y | Y | Exon |
*
Probes subjected to validation using quantitative pyrosequencing. Of the initial 20 loci listed, 11 were not able to be assessed due to technical limitations regarding probe design and performance.