The human pan-cancer methylation database, MethHC is a web based resource focused on the DNA methylation of human diseases. MethHC integrated data such as DNA methylation, gene expression, microRNA methylation, microRNA expression, and the correlation of methylation and gene expression from TCGA (The Cancer Genome Atlas)
DNA methylation is an important epigenetic regulator of gene transcription and a lot of reports have demonstrated that genes with high levels of DNA methylation in their promoter region are transcriptionally silent. DNA methylation is adding a methyl group to cytosine, typically occurring in CpG dinucleotides in mammalian.
Currently, MethHC integrated data such as DNA methylation, gene expression, microRNA methylation, microRNA expression, and the correlation of methylation and gene expression from the TCGA (The Cancer Genome Atlas), which includes 18 human cancers over 6,000 samples and 6,548 microarray and 12,567 RNA sequencing data.
Table 1 shows the number of sample for each cancer in MethHC
gives the comparison between the proposed MethHC and other previous database, such as MethDB, PubMeth, MethyCancer, NGSMethDB and DiseaseMeth.
1. MethHC provides the methylation and expression profiles in both genes and microRNAs in 18 human cancers.
2. We offer the methylation level across gene regions (promoter,enhancer, TSS1500, TSS200, 5'UTR, first exon, gene body and 3'UTR), as well as CpG islands/CPG island regions, shelves and shores.
Schematic diagram of gene regions and CpG Island regions
3. We integrate 6,548 microarray and 12,567 RNA sequencing data from TCGA. For each gene, it also shows the correlation between DNA methylation and gene expression. Thus, users could investigate the role of DNA methylation in gene expression.
4. Using Hierarchical clustering graph to offer the methylation patterns in the different cancers.
5. TOP 250 analysis identify 250 hypermethylated genes, 250 hypomethylated genes and 250 most differentially methylated genes in a certain cancer.
Highlights of MethHC
MethHC: a database of DNA methylation and gene expression in human cancer.
W.Y. Huang, S.D. Hsu, H.Y. Huang, Y.M. Sun, C.H. Chou, S.L. Weng, H.D. Huang*
Nucleic Acids Res. 2015 Jan;43(Database issue):D856-61.