DNA Methylation Database (MethDB)

Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract The DNA Methylation Database (MethDB) is a public database dedicated to DNA methylation. It attempts to store all data about DNA methylation in a common source.

MethDB can be searched in different ways, ranging from a simple browse mode to detailed queries for sequence-specific DNA methylation profiles and patterns, total methylation content data or environmental conditions that can influence the methylation state of DNA.

MethDB is an annotated database, and the scientific community is invited to submit their data.

MethDB 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 5-methylcytosine (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.

Structure of the database and file formats --

MethDB was designed to store heterogeneous data from different kinds of experiments. The database system has an open structure which consists of 18 tables and can easily be extended. The tables are related to each other.

The three (3) central tables are ‘sample’, ‘experiment’ and ‘methylation’.

A ‘sample’ record contains the description of the object, or target, of an experiment. In ‘experiment’ the experimental conditions and procedures are stored. The ‘methylation’ table contains the results of the experiments.

When the database was first created, the manufacturer’s distinguished three (3) sorts of results: methylation content, methylation profile and methylation pattern.

1) Methylation content is the relative share of 5mC in a DNA sample without having information about the position of 5mC in the sequence.

2) A methylation profile consists of a series of values for the methylation level at cytosine positions along a known sequence.

3) Methylation patterns describe the sequence of the five (5) nucleotide bases G, A, T, C, and 5mC in individual DNA molecules. DNA sequences, methylation profiles and methylation patterns are stored in flat ASCII format.

Sequences -

Sequences are simple text files in FASTA format (>name [new line] sequence [new line]). The name is the sequence ID. These files contain the investigated sequences in the standard IUB notation.

Methylation profiles -

Methylation profiles are described by tables of two (2) comma-separated values: position in a mother-sequence and degree of methylation at this site between 0 (No methylation) and 1 (complete methylation). ‘na’ instead of the methylation level indicates that the position was Not analyzed and that this fact has been mentioned in the original publication.

Methylation patterns -

Methylation patterns are sequence files in FASTA format with all nucleotide bases, except 5mC, written in lower case and 5-mC residues written in upper case C.

Description of the web interface of MethDB --

The search page offers three (3) forms for a structured search and one for a simple quick-search field.

Search for patterns and profiles -

Methylation patterns (G, A, T, C, 5mC sequences) and methylation profiles (level of methylation at cytosine sites across a sequence) are sequence specific data.

It is possible to search the database for species, sex, tissue and a gene or locus. A table is returned with a list of matching records.

The [Details]-link brings the user to a page with specific information about the particular experiment and the methylation profile or a list of methylation patterns. By definition, one experiment can deliver several patterns but only one profile.

Multiple experiments can be performed on one sample. If an experimental method is DNA strand specific, the complement DNA strands are treated as separate samples.

Search for 5mC content -

This query form permits you to search for species, sex, tissue, phenotype and DNA type of a sample.

The database returns a table of matching records together with their 5mC content data. The [Proof]-link brings the user to the reference for the data, the [Details]-link provides information about the sample and the experimental procedure used to obtain the data.

Search for phenotypes -

This form allows you to enter 5mC content values and to search for phenotypes that have been found to be associated with these 5mC content data.

Note: Provided enough background data is present this form might be useful for diagnostic purposes.

Quick search -

In this simple query form a single search term can be entered. When the query is submitted a full text search is performed in the following fields: comment, method name, sample name, restriction enzyme, author, phenotype, tissue, gene and species name.

In the resulting table, the most recent entries are listed first.

MethDB contains a number of cross references to other databases, for instance the NCBI Taxonomy browser, Entrez PubMed, Entrez GenBank and OMIM and independent web-sites.

Submission policy and prospects of the MethDB database --

Related literature is screened and the available data are entered into the database. Each time literature data has been entered; the corresponding authors of the original research papers are informed and asked to verify these entries.

Data from unpublished sources can be submitted by personal communication to the database administrator.

The manufacturers would like to invite and encourage the scientific community to submit their findings. Naturally, for every database entry the author who has submitted the data is indicated.

The short-term goal of the MethDB project is to collect as much data as possible and to make these data available to the public.

The manufacturers believe that as soon as a sufficient amount of data has been accumulated it will be possible to gain new insights about the function of DNA methylation in the living cell.

Note: The MethDB database is designed to store methylation data. No analysis tools are included.

However, external tools are available and users are invited to develop further software for the analysis of methylation patterns.

See the manufacturer’s web-site for additional info and access to MethTools 2.0 - online analysis of bisulfite data.

System Requirements

Web-based

Manufacturer

Manufacturer Web Site DNA Methylation Database (MethDB) or DNA Methylation Database (MethDB)

Price Contact manufacturer.

G6G Abstract Number 20762

G6G Manufacturer Number 104341