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PubMeth: a cancer methylation database combining text-mining and expert annotation.

Maté Ongenaert1, Leander Van Neste, Tim De Meyer

  • 1Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Laboratory for Bioinformatics and Computational Genomics, Ghent University, B-9000 Ghent, Belgium. mate.ongenaert@ugent.be

Nucleic Acids Research
|October 13, 2007
PubMed
Summary

PubMeth is a cancer methylation database that provides a summarized overview of DNA methylation data. It aids researchers by consolidating gene methylation information across various cancer types for easier access and analysis.

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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
07:50

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Published on: September 18, 2020

Area of Science:

  • Genomics
  • Cancer Research
  • Bioinformatics

Background:

  • DNA methylation is a key epigenetic mechanism involved in gene regulation.
  • Aberrant DNA methylation patterns are frequently observed in various cancer types.
  • A comprehensive, curated database is needed to manage the growing volume of cancer methylation data.

Purpose of the Study:

  • To develop PubMeth, a cancer methylation database.
  • To provide an annotated, reviewed, sorted, and summarized overview of available DNA methylation data.
  • To facilitate research on gene methylation in cancer.

Main Methods:

  • Text-mining of Medline/PubMed abstracts for gene methylation information.
  • Manual curation and annotation of selected abstracts to ensure specificity and quality.
  • Development of a query system based on genes or cancer types.

Main Results:

  • PubMeth includes genes reported as methylated in diverse cancer types.
  • The database allows querying by specific genes to identify associated cancer types.
  • It also enables searching by cancer type to find relevant methylated genes.
  • The integrated text-mining and manual curation approach enhances data accuracy and speed.

Conclusions:

  • PubMeth offers a valuable, freely accessible resource for cancer methylation research.
  • The database streamlines the process of identifying and analyzing gene methylation markers in cancer.
  • It supports researchers in understanding epigenetic alterations in tumorigenesis.