MethHC: a database of DNA methylation and gene expression in human cancer

Abstract

We present MethHC (http://MethHC.mbc.nctu.edu.tw), a database comprising a systematic integration of a large collection of DNA methylation data and mRNA/microRNA expression profiles in human cancer. DNA methylation is an important epigenetic regulator of gene transcription, and genes with high levels of DNA methylation in their promoter regions are transcriptionally silent. Increasing numbers of DNA methylation and mRNA/microRNA expression profiles are being published in different public repositories. These data can help researchers to identify epigenetic patterns that are important for carcinogenesis. MethHC integrates data such as DNA methylation, mRNA expression, DNA methylation of microRNA gene and microRNA expression to identify correlations between DNA methylation and mRNA/microRNA expression from TCGA (The Cancer Genome Atlas), which includes 18 human cancers in more than 6000 samples, 6548 microarrays and 12 567 RNA sequencing data.

Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma

“…We examined DNA methylation of the HEXIM1 locus using MethHC (Huang et al, 2015) to analyze melanoma methylation data from The Cancer Genome Atlas (TCGA). The HEXIM1 promoter is hypermethylated in tumor samples, suggesting that hypermethylation downregulates HEXIM1 (Figure 1D).…”

EphB1 Suppression in Acute Myelogenous Leukemia: Regulating the DNA Damage Control System

“…The tumor-suppressor function of EphB1 in AML and the association in a variety of cancers between loss of expression and aggressive tumor phenotypes implies that EphB1 is an important regulator of common cancer cell–transforming pathways (12, 13, 34). Conformingly, we used the MethHC DNA methylation database in human cancers (35) to analyze EphB1 promoter CpG site methylation and found common promoter hypermethylation enriched at the 5′ untranslated regions (Supplementary Fig. S3, all cancers P < 0.005).…”

MethSurv: A Web Tool to Perform Multivariable Survival Analysis Using DNA Methylation Data

“…Although single CpG methylation patterns might be a potential biomarker for cancer risk assessment [35], it has also been suggested that different genomic regions can be associated with differential survival prognosis [36]. Moreover, several recently published web tools emphasize the need for analyzing DNA methylation data based on sub-regions [9,10]. Therefore, we provide the users with a detailed overview of individual CpG sites with the options to select genomic regions (relative to CGI and gene sub-region), methods to establish cut-off points for dichotomizing higher and lower methylation patient groups (mean, median, lower quantile, upper quantile and maxstat) and adjustment type.…”

“…However, analyzing the raw data from such consortia is a labor-intensive and time-consuming process that requires specific bioinformatics skills. Multiple public resources such as Wanderer [9], METHHC [10] and MEXPRESS [11] provide a simple user interface to explore the relationship between methylation and gene expression data originating from TCGA. Additionally, tools to perform survival analysis using gene expression data from TCGA are also available to the research community [12][13][14][15][16][17][18][19][20].…”