RE type | RE location (hg19)a | Proximal gene symbol | Distance to proximal gene (bp) | Genomic region | Differential methylation analysis (HCV-HCC vs normal) | RE methylation vs gene expression correlation analysis | Differential gene expression analysis (HCV-HCC vs normal) | Directionally consistent | |||
---|---|---|---|---|---|---|---|---|---|---|---|
Mean difference | p value | Max. Correlationb | Min. p valueb | log2 fold change | p value | ||||||
LINE-1 | chr10:134875427–134876211 | ADGRA1 | 25,296 | Intergenic | − 0.331 | 6.97E−07 | − 0.23 | 0.613 | − 3.358 | 0.004 | No |
LINE-1 | chr6:9810984–9817010 | N/A c | N/Ac | Intergenic | − 0.203 | 1.23E−06 | N/Ac | N/Ac | N/Ac | N/Ac | N/Ac |
LINE-1 | chr7:4388884–4389235 | SDK1 | 80,252 | Intergenic | − 0.382 | 1.08E−07 | 0.62 | 0.008 | − 0.018 | 0.980 | Yes |
LINE-1 | chr7:4085177–4085587 | SDK1 | 0 | Intronic | − 0.365 | 3.29E−06 | 0.33 | 0.161 | − 0.018 | 0.980 | Yes |
LINE-1 | chr7:157594780–157595648 | PTPRN2 | 0 | Intronic | − 0.385 | 4.40E−05 | 0.72 | 0.004 | − 1.053 | 0.116 | Yes |
LINE-1 | chr11:2499185–2499531 | KCNQ1 | 0 | Intronic | − 0.408 | 1.83E−05 | 0.53 | 0.034 | 1.343 | 0.076 | No |
LINE-1 | chr5:8084329–8090357 | MTRR | 183,093 | Intergenic | − 0.168 | 1.47E−05 | −0.51 | 0.044 | 0.062 | 0.866 | Yes |
LINE-1 | chr2:242938503–242938722 | LINC01237 | 0 | Intronic | − 0.337 | 1.18E−05 | 0.28 | 0.274 | 0.764 | 0.344 | No |
LINE-1 | chr7:157318533–157319261 | PTPRN2 | 12,488 | Intergenic | − 0.443 | 2.19E−09 | 0.67 | 0.003 | − 1.053 | 0.116 | Yes |
LINE-1 | chr8:142852678–142853054 | MROH5 | 335,347 | Intergenic | − 0.409 | 2.99E−05 | −0.54 | 0.269 | 0.573 | 0.737 | Yes |
LINE-1 | chr8:143458657–143458848 | TSNARE1 | 0 | Intronic | 0.107 | 2.73E−05 | 0.58 | 0.020 | 0.960 | 0.013 | Yes |
LINE-1 | chr2:1166233–1166668 | SNTG2 | 0 | Intronic | − 0.276 | 1.44E−05 | 0.82 | 0.047 | − 0.102 | 0.955 | Yes |
Alu | chr13:30062564–30062769 | MTUS2 | 0 | Intronic | − 0.275 | 9.85E−07 | 0.52 | 0.156 | − 3.564 | 0.335 | Yes |
Alu | chrX:103294139–103294294 | H2BFM | 222 | Promoterd | − 0.390 | 1.13E−06 | N/Ae | N/Ae | N/Ae | N/Ae | N/Ae |
Alu | chr6:31598686–31598816 | PRRC2A | 0 | Intronic | 0.137 | 2.90E−06 | 0.25 | 0.284 | 1.089 | 0.001 | Yes |