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Table 2 Functional analysis of HCV-HCC-associated dmRE in TCGA

From: DNA methylation of individual repetitive elements in hepatitis C virus infection-induced hepatocellular carcinoma

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
  1. aRanked by statistical significance, within LINE-1 and Alu, respectively
  2. bMaximum magnitude of correlation and minimum p values across the CpGs in the RE
  3. cNo proximal gene identified within 500 kbp
  4. dWithin 2000 bp upstream of the transcription start site
  5. eExtremely low expression across samples