Table 3.
Methylation of different genes reported in individual studies
| Gene | Name | Function | Tumor type | Method | Samples | Methylation range (%) |
|---|---|---|---|---|---|---|
| ADAM23 | ADAM metallopeptidase domain 23 | Cell–cell and cell–matrix interactions | LC (Calmon et al. 2007) | MSP (Calmon et al. 2007) | T (Calmon et al. 2007) | 42 |
| ADAMTS18 | A disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18 | Tumor suppression | NPC (Jin et al. 2007) | MSP (Jin et al. 2007) | (T,NE) (Jin et al. 2007) | 70 |
| AIM1 | Absent in melanoma 1 | Tumor suppression | NPC (Loyo et al. 2011) | QMSP (Loyo et al. 2011) | T (Loyo et al. 2011) | 30 |
| APAF1 | Apoptotic peptidase activating factor 1 | Apoptosis | LC (Huang et al. 2004) | MSP (Huang et al. 2004) | T (Huang et al. 2004) | 40 |
| ATM | Ataxia telangiectasia mutated | Regulating DNA damage response mechanism | HNC (Ai et al. 2004) | MSP (Ai et al. 2004) | (T,NE) (Ai et al. 2004) | 25 |
| BMP2A | Bone morphogenetic protein 2A | Induction of cartilage and bone formation | HNSCC (Tokumaru et al. 2004) | BS (Tokumaru et al. 2004) | T (Tokumaru et al. 2004) | 25 |
| C/EBPalpha | Tumor suppressor CCAAT enhancer binding protein alpha | Transcriptional regulation | HNC (Bennett et al. 2007) | COBRA (Bennett et al. 2007) | (T,MN) (Bennett et al. 2007) | 68 |
| CALCA | Calcitonin-related polypeptide alpha | Calcium regulation and phosphorus metabolism | NPC (Loyo et al. 2011) | QMSP (Loyo et al. 2011) | T (Loyo et al. 2011) | 44 |
| CHD13 | Cadherin 13 | Calcium-dependent cell adhesion | NPC (Sun et al. 2007) | MSP (Sun et al. 2007) | (T,NE) (Sun et al. 2007) | 89.7 |
| CRABP2 | Cellular retinoic acid binding protein 2 | Retinoic acid-mediated regulation of human skin growth and differentiation | HNSCC (Calmon et al. 2009) | MSP (Calmon et al. 2009) | (T,L) (Calmon et al. 2009) | 58 |
| CRBPI | Cellular retinol-binding protein type I | Intracellular transport of retinol | NPC (Kwong et al. 2005b) | MSP (Kwong et al. 2005b) | T (Kwong et al. 2005b) | 87.8 |
| CRBPIV | Cellular retinol-binding protein type IV | Intracellular transport of retinol | NPC (Kwong et al. 2005b) | MSP (Kwong et al. 2005b) | T (Kwong et al. 2005b) | 54 |
| CYGB | Cytoglobin | Transfer of oxygen from arterial blood to the brain | OSCC (Shaw et al. 2006) | PS (Shaw et al. 2006) | (T,MN) (Shaw et al. 2006) | 65 |
| CYP1A1 | Cytochrome p450 family 1A | Carcinogen metabolism | HNC (Sharma et al. 2010) | MSP (Sharma et al. 2010) | (T,NE) (Sharma et al. 2010) | 39.7 |
| CYP2A13 | Cytochrome P450, family 2, subfamily A, polypeptide 13 | Carcinogen metabolism | HNC (Sharma et al. 2010) | MSP (Sharma et al. 2010) | (T,NE) (Sharma et al. 2010) | 27.4 |
| DAB2 | Human disabled-2 | Signal transduction | NPC (Tong et al. 2010) | MSP (Tong et al. 2010) | T (Tong et al. 2010) | 65 |
| DBCCR1 | Deleted in bladder cancer 1 | Inhibition of cell proliferation, involvement in cell death, and regulation of plasminogen pathway | (OSCC, PM-OCL) (Gao et al. 2004) | MSP (Gao et al. 2004) | (T,MN) (Gao et al. 2004) | 44 |
| EpCAM | Epithelial cell adhesion molecule | Homotypic calcium-independent cell adhesion | OSCC (Shiah et al. 2009) | MSP (Shiah et al. 2009) | T (Shiah et al. 2009) | 51 |
| ESR | Estrogen receptor alpha | Hormone binding, DNA binding and activation of transcription | NPC (Loyo et al. 2011) | QMSP (Loyo et al. 2011) | T (Loyo et al. 2011) | 26 |
| FancB | Fanconi anemia, complementation group B | DNA repair | HNSCC (Smith et al. 2010) | QMSP (Smith et al. 2010) | (T,NE) (Smith et al. 2010) | 31 |
| GALR1 | Galanin receptor 1 | Tumor suppression | HNSCC (Misawa et al. 2008) | (MSP, BS) (Misawa et al. 2008) | T (Misawa et al. 2008) | 38 |
| GNAT1 | Guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1 | Signal transduction | NPC (Yi et al. 2007) | MSP (Yi et al. 2007) | (T,CINT) (Yi et al. 2007) | 100 |
| GSTM1 | Glutathione S-transferase mu 1 | Carcinogen metabolism | HNC (Sharma et al. 2010) | MSP (Sharma et al. 2010) | (T,NE) (Sharma et al. 2010) | 58.1 |
| HIC1 | Hypermethylated in cancer 1 | Transcriptional regulation | HNSCC (El-Naggar et al. 1997) | MSP (El-Naggar et al. 1997) | T (El-Naggar et al. 1997) | 95 |
| HRASLS | HRAS-like suppressor | Formation of peripheral nerve trajectories | NPC (Yanatatsaneejit et al. 2008) | MSP-COBRA (Yanatatsaneejit et al. 2008) | (T,NE,L) (Yanatatsaneejit et al. 2008) | 17 |
| IKKalpha | IkappaB kinase-alpha | NF-kappaB signaling pathway | OSCC (Maeda et al. 2007b) | BS (Maeda et al. 2007b) | (T,NE) (Maeda et al. 2007b) | 63 |
| IRF8 | Interferon regulatory factor 8 | Transcriptional regulation | NPC (Lee et al. 2008) | MSP (Lee et al. 2008) | T (Lee et al. 2008) | 78 |
| LARS2 | Leucyl-tRNA synthetase 2, mitochondrial | The action of a catalyst charging of tRNALeu(UUR) with leucine | NPC (Zhou et al. 2009) | PCR-SSCP (Zhou et al. 2009) | T (Zhou et al. 2009) | 64 |
| LHX6 | LIM homeobox 6 | The specification of cortical interneuron subtypes and in the migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex | HNC (Estécio et al. 2006) | (MS/AP-PCR) (Estécio et al. 2006), (COBRA) (Estécio et al. 2006) | (T,NE) (Estécio et al. 2006) | 65.6 |
| LRP1B | Low-density lipoprotein receptor-related protein 1B | Process of receptor-mediated endocytosis | OSCC (Nakagawa et al. 2006) | COBRA (Nakagawa et al. 2006) | T (Nakagawa et al. 2006) | 43 |
| LTF | Lactotransferrin | Antimicrobial activity | NPC (Yi et al. 2006) | MSP (Yi et al. 2006) | (T,CINT) (Yi et al. 2006) | 63.6 |
| MALT1 | Mucosa-associated lymphoid tissue 1 | Signal transduction | OSCC (Chiba et al. 2009) | MSP (Chiba et al. 2009) | (T,NE) (Chiba et al. 2009) | 83 |
| MINT2 | Methylated in tumor-2 | Tumor suppression | OSCC (Ogi et al. 2002) | MSRE (Ogi et al. 2002) | T (Ogi et al. 2002) | 8 |
| MINT27 | Methylated in tumor-27 | Tumor suppression | OSCC (Ogi et al. 2002) | MSRE (Ogi et al. 2002) | T (Ogi et al. 2002) | 16 |
| MIPOL1 | Mirror-image polydactyly 1 | Tumor suppression | NPC (Cheung et al. 2009) | MSP (Cheung et al. 2009) | (T,MN) (Cheung et al. 2009) | 63 |
| MT1G | Metallothionein 1G | Response to heavy metals | HNSCC (Tokumaru et al. 2004) | BS (Tokumaru et al. 2004) | T (Tokumaru et al. 2004) | 25 |
| MTNR1A | Melatonin receptor 1 A | Reproductive and circadian actions of melatonin | OSCC (Nakamura et al. 2008) | (COBRA, MSP) (Nakamura et al. 2008) | (T,MN) (Nakamura et al. 2008) | 62 |
| MX1 | Myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse) | Regulation of the calcium channel activity of TRPCs and activation against influenza virus and VSV, a rhabdovirus | HNSCC (Calmon et al. 2009) | MSP (Calmon et al. 2009) | (T,L) (Calmon et al. 2009) | 46 |
| NDRG2 | N-myc downstream-regulated gene 2 | Neurite outgrowth | (OSCC, PM-OCL) (Furuta et al. 2010) | MSP (Furuta et al. 2010) | T (Furuta et al. 2010) | 80 |
| NISCH | Nischarin | Membrane-associated mediator of the I1R signaling | HNSCC (Hoque et al. 2008) | QMSP (Hoque et al. 2008) | T (Hoque et al. 2008) (SA-H,NE) (Hoque et al. 2008) | 36 |
| NmU | Neuromedin U | Stimulation of contractions of the ileum and urinary bladder | HNSCC (Tokumaru et al. 2004) | BS (Tokumaru et al. 2004) | T (Tokumaru et al. 2004) | 20 |
| OGDHL | Oxoglutarate dehydrogenase-like | Citric acid cycle | HNSCC (Hoque et al. 2008) | QMSP (Hoque et al. 2008) | T (Hoque et al. 2008) (SA-H,NE) (Hoque et al. 2008) | 8 |
| PAK3 | p21-activated protein kinase 3 | Cytoskeleton reorganization and nuclear signaling | HNSCC (Hoque et al. 2008) | QMSP (Hoque et al. 2008) | T (Hoque et al. 2008) (SA-H,NE) (Hoque et al. 2008) | 52 |
| PCDH10 | Protocadherin 10 | Calcium-dependent cell adhesion | NPC (Ying et al. 2006) | MSP (Ying et al. 2006) | T (Ying et al. 2006) | 82 |
| PRTFDC1 | Phosphoribosyl transferase domain containing 1 | Tumor suppression | OSCC (Suzuki et al. 2007) | COBRA (Suzuki et al. 2007) | T (Suzuki et al. 2007) | 17 |
| RASSF4 | Ras association (RalGDS/AF-6) domain family member 4 | Tumor suppression | HNSCC (Steinmann et al. 2009) | COBRA (Steinmann et al. 2009) | (T,MN) (Steinmann et al. 2009) | 13 |
| RASSF5 | Ras association (RalGDS/AF-6) domain family member 5 | Tumor suppression | HNSCC (Steinmann et al. 2009) | COBRA (Steinmann et al. 2009) | (T,MN) (Steinmann et al. 2009) | 58 |
| RB1 | Retinoblastoma 1 | Tumor suppression | SGC (Kishi et al. 2005) | MSP (Kishi et al. 2005) | T (Kishi et al. 2005) | 41.7 |
| RECK | Reversion-inducing cysteine-rich protein with kazal motifs | Suppression of tumor invasion and metastasis | OSCC (Long et al. 2008) | MSP (Long et al. 2008) | (T,MN,NE) (Long et al. 2008) | 52 |
| RIZ1 | Retinoblastoma protein-interacting zinc finger protein | Transcriptional activation | NPC (Chang et al. 2003a) | MSP (Chang et al. 2003a) | (T, L,SA-P) (Chang et al. 2003a) | 60 |
| ROBO1 | Roundabout, axon guidance receptor, homolog 1 (Drosophila) | Tumor suppression | (HNSCC) (Ghosh et al. 2009) (PM-HNL) (Ghosh et al. 2009) | MSRE (Ghosh et al. 2009) | T (Ghosh et al. 2009) | 21 |
| SFRP2 | Secreted protein 2 | Inhibition of Wnt signaling | OSCC (Sogabe et al. 2008) | MSP (Sogabe et al. 2008) | (T, MN) (Sogabe et al. 2008) | 36 |
| SFRP5 | Secreted protein 5 | Inhibition of Wnt signaling | OSCC (Sogabe et al. 2008) | MSP (Sogabe et al. 2008) | (T, MN) (Sogabe et al. 2008) | 16 |
| SOCS3 | Suppressor of cytokine signaling 3 | Signal transduction | (HNC, PM-HNC) (Weber et al. 2005) | MSP (Weber et al. 2005) | (T,MN,LN) (Weber et al. 2005) | 90 |
| STAT1 | Signal transducer and activator of transcription 1 | Signal transduction | HNC (Xi et al. 2006) | MSP (Xi et al. 2006) | (T,L) (Xi et al. 2006) | 75 |
| SYK | Spleen tyrosine kinase | Signal transduction | OSCC (Ogane et al. 2009) | QMSP (Ogane et al. 2009) | (T,MN) (Ogane et al. 2009) | 63 |
| TGFBR-I | Transforming growth factor, beta receptor 1 | Signal transduction | HNSCC (Muñoz-Antonia et al. 2009) | MSP (Muñoz-Antonia et al. 2009) | T (Muñoz-Antonia et al. 2009) | 62 |
| TCF21 | Transcription factor 21 | Epithelial–mesenchymal interactions | HNC (Smith et al. 2006) | COBRA (Smith et al. 2006) | (T,MN) (Smith et al. 2006) | 76 |
| TSC2 | Tuberous sclerosis 2 | Tumor suppression | OSCC (Chakraborty et al. 2008) | COBRA (Chakraborty et al. 2008) | (T,MN) (Chakraborty et al. 2008) | 100 |
| TSLC1 | Tumor suppressor in lung cancer | Tumor suppression | NPC (Hui et al. 2003) | MSP (Hui et al. 2003) | (T,NE) (Hui et al. 2003) | 34.2 |