Go to the abstract in the NAR 2001 Database Issue.
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Institut de Genetique humaine (CNRS 1142) 141 rue de la Cardonille 34396 Montpellier FRANCE
Contact cgrunau@igh.cnrs.fr
Methylation of cytosine in the 5 position of the pyrimidine ring is a major modification of the DNA in most organisms. In eucaryotes, the distribution and number of 5-methylcytosines (5mC) along the DNA is heritable but can also change with the developmental state of the cell and as a response to modifications of the environment. DNA methylation has probably a number of functions, but the scientific interest has recently focused on the gene silencing effect methylation can have in eucaryotic cells. In particular, the discovery of changes of the methylation level during cancer development has increased the interest in this field. In a rapid changing world the availability of information is a crucial factor for success. Biologists, physician and biomedical researchers have been among the first to establish catalogs and databases in electronic form and to make them available on the world-wide-web. During the last 20 years a large amount of data about DNA methylation has been accumulating but so far no attempt had been made to collect and store these published or unpublished methylation data in a public database. For this reason we established a public database for DNA methylation and propose to store all available information in this database (http://www.methdb.de). The database contains currently methylation patterns, profiles and total methylation content data for 41 species, 117 tissues and 56 phenotypes coming from a total of 1432 experiments. More than half of the data for human tissues refers to DNA methylation in cancer cells. By their very nature, methylation data are very heterogenous in form ranging from percentage of methylation in total DNA to methylation patterns with single-base and single-molecule resolution. The database was designed to unify these data and to convert them - if possible - into a comparable format. The database stores information about the origin of the investigated sample and the experimental procedure, and contains the DNA methylation data. Query masks allow for searching for 5mC content, species, tissue, gene, sex, phenotype, sequence ID and DNA type. The output lists all available information including the relative gene expression level. DNA methylation patterns and methylation profiles are shown both as a graphical representation and as G/A/T/C/5mC-sequences or tables with sequence positions and methylation levels, respectively. At the moment, few of our entries are related to the impact of diet and environmental factors on DNA methylation. One of our major interests is to strengthen this part of the database. Further development of MethDB will also be focused on improved data analysis and submission tools (http://genome.imb-jena.de/methtools/). As a public database, MethDB relies on submissions and users are invited to send their data to MethDB either by e-mail or surface mail.
- PCR conditions
The database was supported by a grant of the Klaus-Tschira-Foundation Heidelberg (Germany).
Category Gene Expression
Go to the abstract in the NAR 2001 Database Issue.