Table 1. AC and CC overlapping methylated genes.
| Gene Symbol | Product | Function/Association with Disease | CpG Number a | Mean Beta value in Cervix | Mean Beta value in Anus | Known Epigenetic/Methylation association with Disease | Genomic Region | Directionality | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Normal | Cx SCC | Difb | q-valuec | Normal | Anal SCC | Difb | q-valuec | |||||||
| ASCL1 | Achaete-scute family bHLH transcription factor 1. Other aliases: BHLHa46; ASH-1; | Transcription factor: accessing closed chromatin and activate neural pathways. Essential for neurons. Mutation in Neuroblastoma. | cg02246645 | 0.053 | 0.461 | 0.408 | 9.8E-04 | 0.138 | 0.482 | 0.344 | 1.4E-04 | Among a panel of methylated genes for the detection of oral SCC | 1stExon | Hypermethylated |
| cg27420520 | 0.007 | 0.422 | 0.415 | 9.2E-04 | 0.074 | 0.408 | 0.333 | 4.6E-05 | ||||||
| cg20718350 | 0.026 | 0.529 | 0.503 | 4.3E-04 | 0.158 | 0.509 | 0.351 | 5.3E-04 | ||||||
| cg03700449 | 0.054 | 0.527 | 0.473 | 4.0E-04 | 0.144 | 0.507 | 0.363 | 3.6E-05 | ||||||
| cg22356339 | 0.036 | 0.520 | 0.484 | 6.9E-06 | 0.143 | 0.420 | 0.276 | 6.4E-05 | ||||||
| ATP10A | ATPase phospholipid transporting 10A (putative) | It is a protein coding gene. Diseases associated with ATP10A include Angelman Syndrome and Angelman Syndrome Due to Imprinting Defect In 15Q11-Q13. Possible imprinted gene. | cg20174066 | 0.119 | 0.565 | 0.446 | 3.5E-04 | 0.276 | 0.509 | 0.232 | 8.8E-04 | Modification of CpG sites in ATP10A genes after hypocaloric-diet-induced weight loss. | 1stExon; 5’UTR; TSS200 | Hypermethylated |
| cg03419058 | 0.028 | 0.568 | 0.540 | 7.5E-04 | 0.212 | 0.587 | 0.375 | 3.7E-04 | ||||||
| cg16389285 | 0.005 | 0.407 | 0.401 | 1.2E-03 | 0.101 | 0.401 | 0.299 | 9.4E-05 | ||||||
| cg20124450 | 0.019 | 0.463 | 0.444 | 8.5E-04 | 0.159 | 0.467 | 0.307 | 4.7E-04 | ||||||
| cg22113930 | 0.043 | 0.516 | 0.473 | 1.2E-03 | 0.215 | 0.522 | 0.307 | 3.0E-04 | ||||||
| cg26230285 | 0.012 | 0.497 | 0.484 | 7.5E-04 | 0.163 | 0.521 | 0.358 | 3.4E-04 | ||||||
| CCDC81 | Coiled-Coil Domain-Containing Protein 81 | It is a Protein Coding gene associated with Brain Cancer; specifically, Ganglioneuroblastoma. | cg18282849 | 0.060 | 0.584 | 0.524 | 7.5E-06 | 0.176 | 0.498 | 0.323 | 1.7E-07 | Hypermethylated in Endometrial Tumors | 1stExon; 5’UTR; TSS200 | Hypermethylated |
| cg10395685 | 0.121 | 0.546 | 0.425 | 2.7E-06 | 0.266 | 0.577 | 0.310 | 2.9E-06 | ||||||
| cg18121003 | 0.141 | 0.672 | 0.531 | 8.9E-07 | 0.264 | 0.564 | 0.301 | 3.8E-07 | ||||||
| cg23817893 | 0.159 | 0.635 | 0.476 | 1.6E-07 | 0.311 | 0.596 | 0.285 | 1.5E-05 | ||||||
| cg04573398 | 0.426 | 0.832 | 0.406 | 1.0E-05 | 0.754 | 0.830 | 0.076 | 9.2E-03 | ||||||
| DPP10 | Dipeptidyl Peptidase Like 10. Other aliases: DP IV-related protein 3 (DPRP3) | May be associated with colorectal cancer. Seen in Autism, mood disorder or schizophrenia. |
cg04075191 | 0.137 | 0.593 | 0.456 | 3.1E-04 | 0.225 | 0.558 | 0.333 | 3.9E-06 | Methylated in nicotine-exposed fetal lung and placental tissue. | Body;1stExon;5’UTR | Hypermethylated |
| cg01718116 | 0.124 | 0.547 | 0.424 | 5.2E-05 | 0.237 | 0.579 | 0.342 | 2.6E-05 | ||||||
| cg00089091 | 0.188 | 0.617 | 0.429 | 1.3E-06 | 0.353 | 0.680 | 0.326 | 7.6E-05 | ||||||
| cg13777681 | 0.039 | 0.582 | 0.543 | 5.2E-04 | 0.185 | 0.670 | 0.486 | 1.2E-04 | ||||||
| FMN2 | Formin 2 | Critical regulator of p21/cell cycle progression | cg15748490 | 0.054 | 0.432 | 0.379 | 2.8E-03 | 0.143 | 0.466 | 0.323 | 3.5E-06 | Associated with parathyroid glioblastoma, retinoblastoma chondrosarcoma. | 5’UTR; 1stExon; TSS200; TSS1500 | Hypermethylated |
| cg19591056 | 0.068 | 0.556 | 0.488 | 8.5E-05 | 0.231 | 0.564 | 0.333 | 5.9E-06 | ||||||
| cg01535698 | 0.021 | 0.442 | 0.421 | 1.4E-04 | 0.147 | 0.486 | 0.339 | 4.1E-04 | ||||||
| cg02574509 | 0.054 | 0.458 | 0.404 | 2.4E-04 | 0.135 | 0.420 | 0.285 | 2.8E-05 | ||||||
| cg25208017 | 0.017 | 0.592 | 0.576 | 3.5E-05 | 0.147 | 0.607 | 0.460 | 1.2E-04 | ||||||
| MARCH11 | Membrane associated ring-CH-type finger 11; E3 ubiquitin-protein ligase MARCH11 | Modulates lysosomal degradation and delivery. Member of membrane-bound E3 ubiquitin ligases known to add ubiquitin to target lysines in substrate proteins, thereby signaling their intracellular transport. | cg25092681 | 0.044 | 0.444 | 0.400 | 2.3E-04 | 0.142 | 0.466 | 0.324 | 2.6E-05 | Could not find associated disease information on MARCH11. | TSS200; TSS1500 | Hypermethylated |
| cg00339556 | 0.031 | 0.551 | 0.519 | 1.3E-05 | 0.165 | 0.460 | 0.295 | 8.6E-05 | ||||||
| cg01791874 | 0.048 | 0.571 | 0.523 | 1.5E-05 | 0.189 | 0.548 | 0.360 | 2.7E-05 | ||||||
| cg17030173 | 0.151 | 0.665 | 0.514 | 6.3E-07 | 0.293 | 0.588 | 0.295 | 1.1E-04 | ||||||
| cg17712694 | 0.091 | 0.673 | 0.583 | 8.0E-08 | 0.264 | 0.605 | 0.341 | 3.3E-04 | ||||||
| cg16150752 | 0.068 | 0.672 | 0.603 | 3.2E-07 | 0.264 | 0.622 | 0.358 | 6.3E-04 | ||||||
| cg21901718 | 0.047 | 0.561 | 0.514 | 1.9E-05 | 0.182 | 0.496 | 0.314 | 1.9E-04 | ||||||
| cg18325622 | 0.115 | 0.571 | 0.456 | 1.3E-07 | 0.267 | 0.584 | 0.317 | 1.2E-04 | ||||||
| cg23065934 | 0.066 | 0.573 | 0.507 | 4.5E-06 | 0.268 | 0.596 | 0.328 | 8.7E-05 | ||||||
| MIR129-2 | microRNA 1292 | Short non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. | cg15556502 | 0.013 | 0.488 | 0.475 | 9.6E-06 | 0.142 | 0.550 | 0.408 | 1.7E-05 | Tumor suppressive methylated in lymphoid malignancies. associated with Univentricular Heart disorder. | TSS200; Body | Hypermethylated |
| cg14416371 | 0.039 | 0.643 | 0.604 | 1.2E-06 | 0.260 | 0.693 | 0.433 | 1.4E-04 | ||||||
| cg14944647 | 0.044 | 0.478 | 0.434 | 4.2E-06 | 0.151 | 0.525 | 0.374 | 2.4E-05 | ||||||
| cg01939477 | 0.028 | 0.606 | 0.578 | 2.2E-06 | 0.181 | 0.618 | 0.437 | 1.1E-04 | ||||||
| cg16407471 | 0.096 | 0.581 | 0.486 | 3.4E-06 | 0.243 | 0.615 | 0.371 | 6.9E-05 | ||||||
| cg05376374 | 0.034 | 0.603 | 0.569 | 1.7E-07 | 0.162 | 0.546 | 0.384 | 1.6E-04 | ||||||
| cg03365311 | 0.075 | 0.516 | 0.441 | 1.6E-05 | 0.195 | 0.520 | 0.325 | 1.6E-05 | ||||||
| PAX1 | Paired box 1. Other aliases: Paired Domain Gene HuP48 (HuP48), OFC2 | It is a member of the paired box (PAX) family of transcription factors and they play critical roles during vertebral column and fetal development. | cg19054524 | 0.054 | 0.504 | 0.449 | 2.7E-05 | 0.141 | 0.452 | 0.311 | 5.2E-05 | Frequent methylation in HNSCC, silenced by methylation in ovarian and CCs | TSS200; 1stExon; 5’UTR | Hypermethylated |
| cg08448701 | 0.065 | 0.514 | 0.450 | 2.4E-05 | 0.149 | 0.457 | 0.308 | 2.1E-05 | ||||||
| cg01783070 | 0.059 | 0.570 | 0.511 | 1.4E-05 | 0.149 | 0.507 | 0.358 | 1.9E-05 | ||||||
| cg19079845 | 0.103 | 0.537 | 0.434 | 5.0E-06 | 0.191 | 0.494 | 0.302 | 1.1E-05 | ||||||
| PEX5L | Peroxisomal biogenesis factor 5 like. Other aliases: TRIP8b, PEX5R, PXR2, PEX5-Related Protein, | Trafficking of peroxisomal matrix proteins | cg02009585 | 0.119 | 0.570 | 0.450 | 1.5E-05 | 0.264 | 0.579 | 0.315 | 1.1E-03 | Rhizomelic Chondrodysplasia Punctata, Type 5 and Rhizomelic Chondrodysplasia Punctata, Type 2 | TSS200; TSS1500 | Hypermethylated |
| cg23346462 | 0.075 | 0.594 | 0.519 | 8.4E-07 | 0.277 | 0.609 | 0.331 | 1.5E-03 | ||||||
| cg02119363 | 0.054 | 0.496 | 0.443 | 1.0E-05 | 0.218 | 0.483 | 0.265 | 8.7E-04 | ||||||
| cg13473356 | 0.085 | 0.542 | 0.457 | 2.4E-06 | 0.268 | 0.525 | 0.257 | 9.0E-04 | ||||||
| cg04894619 | 0.104 | 0.551 | 0.447 | 7.2E-07 | 0.274 | 0.497 | 0.223 | 1.9E-03 | ||||||
| cg18780412 | 0.030 | 0.559 | 0.529 | 6.5E-05 | 0.209 | 0.537 | 0.329 | 7.9E-04 | ||||||
| cg21176048 | 0.023 | 0.424 | 0.401 | 3.6E-04 | 0.173 | 0.504 | 0.331 | 4.3E-04 | ||||||
| cg05131623 | 0.151 | 0.629 | 0.477 | 2.9E-05 | 0.379 | 0.702 | 0.324 | 1.4E-03 | ||||||
| RYR2 | Ryanodine receptor 2. Other aliases: ARVD2, RYR-2, ARVC2, RyR2, VTSIP2. | Encodes a ryanodine receptor found in cardiac muscle sarcoplasmic reticulum. Mediates cellular calcium release | cg07790615 | 0.045 | 0.565 | 0.520 | 1.4E-04 | 0.218 | 0.617 | 0.398 | 6.2E-07 | Associated with arrhythmogenic right ventricular dysplasia and ventricular tachycardia stress-induced polymorphic 1 | TSS1500, Body | Hypermethylated |
| cg03422911 | 0.258 | 0.673 | 0.415 | 7.7E-06 | 0.457 | 0.701 | 0.243 | 1.5E-04 | ||||||
| cg18375860 | 0.081 | 0.513 | 0.432 | 1.4E-07 | 0.207 | 0.537 | 0.330 | 1.7E-04 | ||||||
| cg11657808 | 0.117 | 0.586 | 0.469 | 7.8E-06 | 0.294 | 0.624 | 0.330 | 8.8E-05 | ||||||
| cg07914084 | 0.057 | 0.547 | 0.490 | 9.0E-05 | 0.207 | 0.565 | 0.358 | 1.8E-04 | ||||||
| SORCS3 | Sortilin related VPS10 domain containing receptor 3. Other aliases: KIAA1059, SORCS | Protein Coding, developing and maturation of the central nervous system. mediate transport from endoplasmic reticulum to Golgi. | cg08495770 | 0.105 | 0.544 | 0.439 | 2.5E-05 | 0.265 | 0.563 | 0.298 | 4.3E-05 | Frequently methylated in gastric cancer. Associated with Alzheimer Disease. | TSS200, 1stExon; 5’UTR | Hypermethylated |
| cg16787600 | 0.071 | 0.547 | 0.476 | 1.3E-05 | 0.213 | 0.533 | 0.320 | 7.8E-05 | ||||||
| cg10778841 | 0.082 | 0.574 | 0.492 | 3.7E-07 | 0.209 | 0.541 | 0.332 | 1.4E-04 | ||||||
| cg18326021 | 0.052 | 0.479 | 0.427 | 1.1E-05 | 0.166 | 0.471 | 0.305 | 8.3E-05 | ||||||
| T | TBXT, T-box transcription factor. Other aliases: T brachyury homolog; LOC292301. | Encodes DNA-binding transcription factor protein; involved with cellular response to retinoic acid. Associated with neural tube defects and chordoma | cg17188046 | 0.111 | 0.551 | 0.440 | 4.3E-05 | 0.252 | 0.623 | 0.371 | 1.1E-04 | No information on methylation and T. | TSS200 | Hypermethylated |
| cg14638883 | 0.107 | 0.520 | 0.413 | 1.8E-05 | 0.276 | 0.534 | 0.257 | 1.6E-03 | ||||||
| cg19675288 | 0.056 | 0.538 | 0.482 | 2.2E-04 | 0.226 | 0.612 | 0.386 | 9.5E-05 | ||||||
| cg06073449 | 0.016 | 0.427 | 0.410 | 1.8E-03 | 0.158 | 0.615 | 0.457 | 4.2E-04 | ||||||
| cg06463958 | 0.039 | 0.589 | 0.550 | 4.2E-04 | 0.241 | 0.667 | 0.426 | 1.4E-04 | ||||||
| WDR17 | WD repeat domain 17 | Plays a functional role in early stages of retinal development. Frequently altered in T cell malignancies. | cg11923920 | 0.148 | 0.629 | 0.481 | 3.8E-07 | 0.237 | 0.487 | 0.251 | 1.0E-03 | Associated with Liver neoplasms, tobacco use and Autosomal recessive retinitis pigmentosa. | 1stExon;5’UTR;1stExon;5’UTR | Hypermethylated |
| cg08095852 | 0.039 | 0.591 | 0.552 | 4.3E-07 | 0.161 | 0.507 | 0.346 | 4.1E-04 | ||||||
| cg27486637 | 0.027 | 0.570 | 0.543 | 4.4E-07 | 0.210 | 0.581 | 0.371 | 1.1E-03 | ||||||
| cg08684639 | 0.039 | 0.577 | 0.537 | 2.2E-04 | 0.118 | 0.547 | 0.429 | 2.0E-05 | ||||||
| ZIK1 | Zinc finger protein interacting with K protein 1 | Basic function unknown | cg00800512 | 0.105 | 0.562 | 0.456 | 1.5E-05 | 0.248 | 0.520 | 0.272 | 1.1E-04 | Methylated biomarker for esophageal SCC. | 5’UTR; 1stExon; TSS200 | Hypermethylated |
| cg12060744 | 0.199 | 0.691 | 0.492 | 4.3E-06 | 0.297 | 0.713 | 0.416 | 3.1E-04 | ||||||
| cg01046104 | 0.084 | 0.644 | 0.560 | 1.9E-07 | 0.322 | 0.697 | 0.374 | 6.1E-04 | ||||||
| cg18579862 | 0.023 | 0.627 | 0.604 | 3.8E-07 | 0.199 | 0.661 | 0.462 | 3.5E-04 | ||||||
| cg26246807 | 0.033 | 0.574 | 0.541 | 1.9E-04 | 0.245 | 0.675 | 0.430 | 6.2E-04 | ||||||
| ZNF154 | zinc finger protein 154. Other aliases: KIAA2003, PHZ-92 | Involved in transcriptional regulation | cg03142586 | 0.033 | 0.504 | 0.471 | 1.2E-03 | 0.200 | 0.444 | 0.244 | 1.2E-03 | Hypermethylation in 15 of 16 distinct cancer types from TCGA | Body; 5’UTR; 1stExon; TSS200 | Hypermethylated |
| cg11294513 | 0.126 | 0.576 | 0.450 | 1.2E-03 | 0.310 | 0.605 | 0.295 | 1.1E-03 | ||||||
| cg05661282 | 0.055 | 0.595 | 0.540 | 7.1E-04 | 0.222 | 0.610 | 0.389 | 4.5E-04 | ||||||
| cg21790626 | 0.030 | 0.523 | 0.494 | 9.1E-04 | 0.160 | 0.481 | 0.321 | 3.4E-04 | ||||||
| cg27049766 | 0.088 | 0.576 | 0.489 | 8.2E-04 | 0.273 | 0.636 | 0.363 | 4.2E-04 | ||||||
| cg03234186 | 0.134 | 0.533 | 0.399 | 1.7E-03 | 0.262 | 0.589 | 0.327 | 4.3E-04 | ||||||
| cg08668790 | 0.133 | 0.583 | 0.450 | 1.3E-03 | 0.291 | 0.631 | 0.340 | 1.2E-04 | ||||||
| cg12506930 | 0.163 | 0.560 | 0.397 | 1.0E-03 | 0.324 | 0.637 | 0.313 | 3.8E-04 | ||||||
| ZNF177 | Zinc finger protein 177 | Involved in transcriptional regulation | cg05928342 | 0.087 | 0.466 | 0.380 | 4.1E-05 | 0.240 | 0.550 | 0.310 | 4.3E-05 | Methylated in gastric and hepatocellular cancer. Promoter methylation frequent in Endometrial cancer. | TSS200 | Hypermethylated |
| cg13703871 | 0.112 | 0.670 | 0.558 | 2.7E-07 | 0.300 | 0.671 | 0.371 | 6.7E-05 | ||||||
| cg08065231 | 0.071 | 0.613 | 0.541 | 5.6E-08 | 0.299 | 0.646 | 0.347 | 2.5E-04 | ||||||
| cg09578475 | 0.153 | 0.730 | 0.577 | 2.2E-08 | 0.456 | 0.724 | 0.268 | 8.1E-04 | ||||||
| cg07788092 | 0.171 | 0.625 | 0.453 | 5.5E-08 | 0.384 | 0.637 | 0.253 | 1.7E-04 | ||||||
| ZNF529 / ZNF382 | Zinc finger protein 529 a.k.a. KIAA1615 | May be involved in transcriptional regulation. Molecular Function: DNA binding | cg25397945 | 0.039 | 0.595 | 0.556 | 1.0E-06 | 0.238 | 0.537 | 0.299 | 2.4E-03 | No information on methylation and ZNF529. | Body; 1stExon; 5’UTR; TSS200; 1stExon; 5’UTR | Hypermethylated |
| cg02587316 | 0.050 | 0.580 | 0.530 | 2.4E-05 | 0.200 | 0.522 | 0.322 | 5.0E-04 | ||||||
| cg18630667 | 0.048 | 0.606 | 0.558 | 1.0E-04 | 0.176 | 0.492 | 0.316 | 3.7E-04 | ||||||
| cg05020604 | 0.036 | 0.586 | 0.550 | 7.6E-05 | 0.195 | 0.504 | 0.310 | 1.9E-04 | ||||||