A database of DNA Methylation and gene expression in Human Cancer

MethHC is a database for Human pan-cancer gene expression, methylation and microRNA expression.


Comparison of MethHC with other methylation databases
Category MethDB PubMeth MethyCancer NGSMethDB DiseaseMeth MENT MethHC
Publication

NAR. 2001

NAR Database Issue (2008)

NAR Database Issue (2008)

NAR Database Issue (2010)

NAR Database Issue (2012)

GENE (2013)

NAR Database Issue (2015)

Last update

2009

-

2008

2014

-

-

2014

Support species

4 species

Homo sapiens

Homo sapiens

6 species

Homo sapiens, 72 diseases

Homo sapiens, 30 tissues

Homo sapiens, 18 cancers

Number of samples

20236 fragments

-

11561 (genes)

Human: 19, Monkey: 6, Tomato: 8, Mouse : 45, Arabidopsis: 27

175 datasets (3610 microarray data)

Methylation: 9,243 microarray data. Gene expression: 34,000 microarray data

Methylation: 6,548 microarray data., Gene expression: 12,567 RNA sequencing data

Number of gene

-

-

11,561

-

-

14,475

20,500, and >1,040 microRNAs

Data sources

Experiments

Medline/PubMed

BIG, MethDB, HEP

GEO

GEO

GEO,TCGA

TCGA

Correlation analysis

NO

NO

YES

YES

YES

YES

YES

microRNA expression

NO

NO

NO

NO

NO

NO

YES

Gene region

NO

NO

CpG Ialand, promoter region

CpG, Promoter region

Promoter region (-1.5K~0.5K)

Probe level only

8 Gene regions+, 5 CpG Island regions*

Other Characteristic

Experimental data only

Automated textmining

Repeat sequence Search

CpG, CHG

Offline analysis, CpG

Differential methylation, Correlation analysis, Sample subtype

microRNA expression, Correlation analysis

+ Including promoter (from -1.5Kb to 0.5Kb of the transcription start site, TSS), TSS1500, TSS200, 5’UTR, enhancer, 1st exon, gene body and 3’UTR gene region
* Including N shelf, N shore, CpG Island, S shelf and S shore of CpG region.