Background
Methods
Animals
Cell lines and treatment
Genomic DNA extraction
RRBS analysis
Alignment of RRBS data and identification of DMCs and DMRs
Bisulfite sequencing
Microarray analysis of gene expression
Real-time PCR analysis
Prediction of the transcription factor binding site
TCGA analysis
Statistical analysis
Results
Genome wide analysis of DNA methylation and gene expression in normal and tumor livers of C3H mice
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 |