Table 2 Description of the 22 CpG islands used to establish the methylation classifier in oral rinse samples
M | CpG island coordinatesa | Number of CpGs covered by the array | Associated gene (ncRNA) | CpG island relationship to gene | Enhancer region | DNase hypersensitivity site | Associated gene functione | Differential methylation in oral/pharyngeal tumor tissuef | |
|---|---|---|---|---|---|---|---|---|---|
FDR-adjusted Q-value | Median differenceg (range) | ||||||||
1 | chr3:15286143-15286274 | 3 | SH3BP5 | 5′UTR: body | True | True | Inhibits phosphorylation activity of Bruton Agammaglobulinemia Tyrosine Kinase; may play a role in BCR-induced apoptosis | 1.12E−07 | −0.19 (−0.35, −0.04) |
2 | chr17:77848690-77848800 | 3 | (JD529337)b |  | True | True |  | 9.86E−09 | −0.14 (−0.17, −0.07) |
3 | chr12:118725604-118725889 | 3 | CIT | Body | True |  | Serine/threonine-protein kinase that plays a role in cell division/cytokinesis | 3.04E−09 | 0.32 (0.13, 0.46) |
4 | chr1:154198084-154198623 | 3 | ARHGEF2 | Body | True | True | Plays a fundamental role in cellular processes initiated by extracellular stimuli via G protein coupled receptors | 4.21E−09 | −0.22 (−0.31, −0.01) |
5 | chr12:28015205-28015607 | 3 | PTHLH | 5′UTR (TSS1500) |  |  | Neuroendocrine peptide member of the parathyroid hormone family that is a critical regulator of cellular and organ growth, development, migration, differentiation, survival, and epithelial calcium ion transport | 3.97E−06 | −0.19 (−0.29, 0.37) |
6 | chr11:2511670-2512178 | 4 | KCNQ1 | Body | True |  | Voltage-gated potassium channel required for the repolarization phase of the cardiac action potential; exhibits tissue-specific imprinting | 3.04E−09 | −0.29 (−0.52, −0.10) |
7 | chr1:8194584-8194818 | 3 | (JD505160) |  | True | True |  | 1.40E−06 | −0.13 (−0.26, 0.09) |
8 | chr12:110319267-110319654 | 4 | (see footnote)c |  |  |  |  | 1.12E−07 | −0.04 (−0.06, 0.01) |
9 | chr5:161207831-161208167 | 4 | GABRA1 | 5′UTR (TSS1500:TSS200) |  |  | Receptor for gamma-aminobutyric acid (GABA), which is the major inhibitory neurotransmitter in the brain | 5.08E−06 | 0.09 (−0.03, 0.66) |
10 | chr19:5538686-5538939 | 3 | SAFB2 | Body |  |  | Binds to scaffold/matrix attachment region (S/MAR) DNA; may function as an estrogen receptor corepressor or inhibitor of cell proliferation | 0.00015 | 0.25 (−0.35, 0.27) |
11 | chr6:25135475-25135786 | 3 | BC070382 d |  |  |  |  | 3.04E−09 | −0.29 (−0.47, −0.04) |
12 | chr10:134072408-134072501 | 3 | PWWP2B | Body: 3′UTR |  |  | PWWP Domain-Containing Protein 2B | 6.28E−08 | 0.21 (−0.10, 0.29) |
13 | chr1:10818517-10818704 | 3 |  |  | True | True |  | 0.00066 | −0.16 (−0.28, 0.19) |
14 | chr1:1385949-1386143 | 5 | ATAD3C | Body |  |  | ATPase Family AAA Domain-Containing Protein 3C | 9.23E−08 | −0.17 (−0.36, 0.03) |
15 | chr10:53743705-53744974 | 7 | DKK1 | 5′UTR: Body |  | TRUE | Member of the dickkopf protein-coding gene family, which play an important role in vertebrate development | 0.59 | −0.02 (−0.10, 0.57) |
16 | chr11:20588323-20588561 | 3 | SLC6A5 | Body | True |  | Solute-carrier transporter involved in the clearance of extracellular glycine during glycine-mediated neurotransmission | 3.51E−06 | −0.03 (−0.06, 0.001) |
17 | chr10:134210902-134211265 | 5 | INPP5A | Body |  |  | Membrane-associated type I inositol 1,4,5-trisphosphate (InsP3) 5-phosphate that mobilizes intracellular calcium and acts as a second messenger for mediating cell responses to various stimuli | 1.89E−07 | −0.09 (−0.42, −0.0004) |
18 | chr5:10702368-10703458 | 3 | ANKRD33B | Body |  |  | Ankyrin Repeat Domain-Containing Protein 33B | 7.67E−09 | 0.14 (0.03, 0.18) |
19 | chr16:85998896-85999172 | 3 | ZCCHC14 | 3′UTR |  | TRUE | Zinc Finger CCHC Domain-Containing Protein 14; interacts with nuclear transcription factors NFIC and NFIX | 0.13 | 0.09 (−0.42, 0.20) |
20 | chr13:105827274-105827476 | 3 | (LINC00460) |  |  |  | (long non-coding RNA of unknown function) | 3.34E−08 | −0.26 (−0.48, 0.04) |
21 | chr5:1010475-1010610 | 3 |  |  | True | True |  | 8.09E−05 | −0.19 (−0.34, 0.11) |
22 | chr2:216945117-216945376 | 6 | MARCH4 | 5′UTR (TSS1 500:TSS200) |  |  | E3 ubiquitin-protein ligase that may mediate ubiquitination of MHC-I and CD4, and promote their subsequent endocytosis and sorting to lysosomes via multivesicular bodies | 0.00076 | −0.04 (−0.06, 0.08) |