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. 2019 Dec 16;9:19148. doi: 10.1038/s41598-019-55453-8

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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(A) Mean β value densities of the tumor(T)/normal(N) samples included in two public HCC datasets (TCGA-LIHC, GSE54503). (B) Smoothed density curves of the genomic index distributions and p-values (two-tailed t-test) for all pairwise comparisons between TCGA-LIHC/GSE54503 datasets and epimarkers (epiHCC1, epiHCC2). (C) Differential β value density of the TCGA-LIHC/GSE54503 datasets and epimarkers (epiHCC1, epiHCC2). (D) Mean genomic index of aberrantly methylated sites |Δβ| ≥ 0.3) in driver genes that have been detected by at least two to five computational methods. (E). Mean genomic index of all TCGA-LIHC and GSE54503 differentially methylated sites compared with the genomic index of COSMIC Tier-1 (T1) cancer gene census. (F). Semantic similarity plot correlating highly-ranked sites of the TCGA-LIHC and GSE54503 datasets, according to MeinteR, with the COSMIC T1, Tier 2 (T2) Gene Census, KEGG HCC pathway, Driver-5 genes and epigenetic markers (epiHCC1, epiHCC2).