Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

Full name:
Description: PubMeth is a cancer methylation database that includes genes that are reported to be methylated in various cancer types.
Year founded: 2008
Last update: 2008-01-01
Version: v1.0
Real time : Checking...
Country/Region: Belgium
Data type:
Data object:
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Contact information

University/Institution: Ghent University
Address: B-9000 Ghent, Belgium
City: Ghent
Country/Region: Belgium
Contact name (PI/Team): Maté Ongenaert
Contact email (PI/Helpdesk):


PubMeth: a cancer methylation database combining text-mining and expert annotation. [PMID: 17932060]
Ongenaert M, Van Neste L, De Meyer T, Menschaert G, Bekaert S, Van Criekinge W.

Epigenetics, and more specifically DNA methylation is a fast evolving research area. In almost every cancer type, each month new publications confirm the differentiated regulation of specific genes due to methylation and mention the discovery of novel methylation markers. Therefore, it would be extremely useful to have an annotated, reviewed, sorted and summarized overview of all available data. PubMeth is a cancer methylation database that includes genes that are reported to be methylated in various cancer types. A query can be based either on genes (to check in which cancer types the genes are reported as being methylated) or on cancer types (which genes are reported to be methylated in the cancer (sub) types of interest). The database is freely accessible at PubMeth is based on text-mining of Medline/PubMed abstracts, combined with manual reading and annotation of preselected abstracts. The text-mining approach results in increased speed and selectivity (as for instance many different aliases of a gene are searched at once), while the manual screening significantly raises the specificity and quality of the database. The summarized overview of the results is very useful in case more genes or cancer types are searched at the same time.

Nucleic Acids Res. 2008:36(Database issue) | 91 Citations (from Europe PMC, 2021-06-19)


All databases:
1130/5061 (77.692%)
Health and medicine:
234/1067 (78.163%)
57/228 (75.439%)
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Record metadata

Created on: 2015-07-28
Curated by:
Shixiang Sun [2016-03-28]
Shixiang Sun [2015-11-22]