Table 2. . Differential methylation between oral and pharyngeal squamous cell carcinoma cell lines and primary non-neoplastic oral epithelial cells.
| CpG-dense region | Associated gene | Head and neck squamous cell carcinoma cell lines | Non-neoplastic oral epithelial cells (referent) | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Cal27 | Detroit562 | FaDu | H413 | |||||||
| Mean % methylation | pdifferential | Mean % methylation | pdifferential | Mean % methylation | pdifferential | Mean % methylation | pdifferential | Mean % methylation | ||
| chr12:118725604–118725889(NCBI36/hg18) | CIT | 89.7% | 0.0005 | 90.4% | 3.83E-05 | 90.9% | 0.0006 | 85.6% | 0.002 | 34.2% |
| chr12:28015205–28015607(NCBI36/hg18) | PTHLH | 0.3% | 0.22 | 15.5% | 0.0008 | 96.0% | 2.48E-07 | 66.1% | 0.0002 | 0.3% |
| chr11:2511670–2512178(NCBI36/hg18) | KCNQ1 | 0.5% | 0.0004 | 8.3% | 5.49E-05 | 1.2% | 0.0002 | 0.7% | 0.0004 | 32.7% |
| chr1:8194584–8194818(NCBI36/hg18) | Intergenic | 0.6% | 0.59 | 3.0% | 0.03 | 0.8% | 0.76 | 1.5% | 0.34 | 0.9% |
| chr12:110319267–110319654(NCBI36/hg18) | Intergenic | 1.2% | 0.91 | 1.5% | 0.83 | 1.2% | 0.91 | 2.6% | 0.28 | 1.3% |
| chr19:5538686–5538939(NCBI36/hg18) | SAFB2 | 94.5% | 0.0008 | 94.5% | 0.0007 | 96.3% | 0.0008 | 91.8% | 3.53E-05 | 70.0% |
| chr6:25135475–25135786(NCBI36/hg18) | Intergenic | 18.0% | 1.33E-05 | 53.6% | 0.0008 | 95.1% | 0.0003 | 64.4% | 0.0008 | 78.0% |
| chr1:10818517–10818704(NCBI36/hg18) | Intergenic | 10.2% | 0.001 | 8.0% | 0.02 | 9.9% | 0.001 | 11.2% | 0.003 | 4.7% |
| chr1:1385949–1386143(NCBI36/hg18) | ATAD3C | 59.8% | 0.04 | 38.3% | 0.01 | 62.3% | 0.02 | 82.2% | 0.0002 | 52.6% |
| chr10:53743705–53744974(NCBI36/hg18) | DKK1 | 0.9% | 0.42 | 0.6% | 0.21 | 0.8% | 0.32 | 1.2% | 0.75 | 1.4% |
| chr11:20588323–20588561(NCBI36/hg18) | SLC6A5 | 2.4% | 0.01 | 4.2% | 0.005 | 5.5% | 0.002 | 3.4% | 0.002 | 1.2% |
| chr10:134210902–134211265(NCBI36/hg18) | INPP5A | 68.7% | 0.002 | 76.1% | 0.16 | 87.3% | 0.12 | 76.0% | 0.09 | 79.2% |
| chr5:10702368–10703458(NCBI36/hg18) | ANKRD33B | 76.3% | 5.10E-07 | 79.1% | 3.08E-07 | 81.3% | 1.15E-07 | 75.6% | 5.53E-05 | 22.0% |
| chr16:85994896–85999172(NCBI36/hg18) | ZCCHC14 | 63.9% | 1.26E-06 | 95.1% | 0.01 | 96.4% | 0.007 | 92.6% | 0.16 | 91.7% |
| chr5:1010475–1010610(NCBI36/hg18) | Intergenic | 4.4% | 4.01E-09 | 57.4% | 1.39E-08 | 78.3% | 2.91E-08 | 60.2% | 3.34E-05 | 24.9% |
| chr2:216945117–216945376(NCBI36/hg18) | MARCH4 | 1.2% | 0.001 | 5.8% | 0.001 | 1.0% | 0.02 | 0.5% | 0.16 | 0.4% |
Significant p-values (<0.05) are highlighted with bold font.
p-values are based on a two-sample t-test for differential methylation of each respective oral and pharyngeal cancer cell line relative to non-neoplastic oral epithelials cells.