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Table 1 Shortlist of the selected genesa

From: The DNA methylation profile of liver tumors in C3H mice and identification of differentially methylated regions involved in the regulation of tumorigenic genes

Associated gene discription DMR position DMR Distance from TSS DMCs number Methylation difference (Tumor -Normal) Gene expression (Tumor / Normal)
ratio p-value
downstream
 Slpi secretory leukocyte protease inhibitor chr2: 164355520–164,355,812 + 697 9 −33.83 408.37 0.0090
 Cela1 chymotrypsin-like elastase family, member 1 chr15: 100687184–100,687,240 + 682 3 −31.23 71.51 0.0003
 Mst1r macrophage stimulating 1 receptor chr9: 107908081–107,908,516 + 1192 13 −46.34 67.47 0.0005
 Btg2 B cell translocation gene 2 chr1: 134077506–134,077,566 + 1591 3 −46.61 18.30 0.0050
 Fgl2 fibrinogen-like protein 2 chr5: 21373036–21,373,583 + 366 10 −31.73 11.88 0.0002
 P2rx7 purinergic receptor P2X chr5: 122644473–122,644,655 + 562 4 −43.12 8.23 0.0031
 Lss lanosterol synthase chr10: 76532531–76,532,879 + 904 8 −59.93 6.17 0.0000
 Grhl1 grainyhead-like 1 chr12: 24573292–24,573,626 + 1005 3 −39.22 6.06 0.0020
 Itm2c integral membrane protein 2c chr1: 85895741–85,895,786 + 1231 3 −31.78 3.91 0.0015
 Chmp6 charged multivesicular body protein 6 chr11: 119915542–119,915,667 + 1732 6 −53.11 2.88 0.0002
 Vasp vasodilator-stimulated phosphoprotein chr7: 19269155–19,269,927 + 1929 14 −40.96 2.27 0.0016
 Mmp14 matrix metallopeptidase 14 chr14: 54433543–54,434,231 + 1939 13 −39.11 2.19 0.0012
 Marveld2 MARVEL domain containing 2 chr13: 100615630–100,615,803 + 1143 2 −34.10 2.06 0.0238
 Pdk2 pyruvate dehydrogenase kinase, isoenzyme 2 chr11: 95039447–95,039,657 + 1716 7 38.16 0.48 0.0034
 Extl1 exostoses-like 1 chr4: 134371099–134,371,620 + 929 44 48.12 0.39 0.0216
 Grm8 glutamate receptor, metabotropic 8 chr6: 28133156–28,133,165 + 1206 3 33.66 0.32 0.0016
 Ppp1r14a protein phosphatase 1, regulatory inhibitor subunit 14A chr7: 29291240–29,291,527 + 1920 8 36.03 0.25 0.0052
 Snx29 sorting nexin 29 chr16: 11405750–11,405,827 + 102 3 60.92 0.22 0.0218
 C8b complement component 8, beta polypeptide chr4: 104767260–104,767,325 + 943 7 54.51 0.18 0.0066
 Igfals insulin-like growth factor binding protein, acid labile subunit chr17: 24880338–24,882,131 + 1568 57 38.73 0.17 0.0003
 Adam11 a disintegrin and metallopeptidase domain 11 chr11: 102762268–102,762,503 + 829 16 54.16 0.16 0.0002
 Cyp8b1 cytochrome P450, family 8, subfamily b, polypeptide 1 chr9: 121914943–121,915,025 + 1279 6 63.26 0.10 0.0231
Upstream
 Ltb lymphotoxin B chr17: 35194367–35,194,502 −4 3 −32.55 20.94 0.0410
 Nfe2 nuclear factor, erythroid derived 2 chr15: 103259509–103,259,588 − 1105 4 −36.04 12.39 0.0045
 Hmgcr 3-hydroxy-3-methylglutaryl-coenzyme A reductase chr13: 96671738–96,671,790 − 801 1 −30.40 4.80 0.0144
 Slc29a1 solute carrier family 29 member 1 chr17: 45600404–45,600,454 − 800 2 37.50 0.37 0.0010
 Slc17a8 solute carrier family 17 chr10: 89621306–89,622,039 −60 7 51.72 0.11 0.0142
  1. aThese genes are hit by PubMed search for the term “cancer” and whose expressions are up- or down-regulated more than 2-fold in an inverse manner compared to the methylation rates between the normal and tumor tissues. Chr: chromosome, DMR: differentially methylated region, DMC: differentially methylated cytosine, TSS: transcription start site. P-values were analyzed by Student’s t-test
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