Literature DB >> 12519951

An improved version of the DNA Methylation database (MethDB).

Céline Amoreira1, Winfried Hindermann, Christoph Grunau.   

Abstract

Cytosine methylation is a characteristic property of prokaryotic and eukaryotic genomes. In the latter, it is indispensable for a healthy development of the organism and uncontrolled changes in the distribution of 5-methylcytosine (5mC) have been linked to severe disorders, in particular cancer. The growing scientific interest in DNA methylation has led to a considerable amount of data about this epigenetic phenomenon. In order to make these data readily available, we have established a dedicated database. The DNA Methylation database (MethDB) is currently the only public database for DNA methylation (http://www.methdb.net). This constantly growing database has become a key resource in the field of DNA methylation research. The database contains currently methylation patterns, profiles and total methylation content data for 46 species, 160 tissues and 72 phenotypes coming from a total of 6667 experiments (as of September 4, 2002). About 14% of the data have not been published elsewhere. These data can be conveniently searched and represented in different ways. Recently, we have included an on-line submission tool that permits the scientific public to directly enter new data into MethDB.

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Year:  2003        PMID: 12519951      PMCID: PMC165540          DOI: 10.1093/nar/gkg093

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  6 in total

1.  DNA Methylation Database "MethDB": a user guide.

Authors:  Christoph Grunau; Eric Renault; Gérard Roizes
Journal:  J Nutr       Date:  2002-08       Impact factor: 4.798

2.  A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.

Authors:  M Frommer; L E McDonald; D S Millar; C M Collis; F Watt; G W Grigg; P L Molloy; C L Paul
Journal:  Proc Natl Acad Sci U S A       Date:  1992-03-01       Impact factor: 11.205

3.  Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE).

Authors:  M L Gonzalgo; P A Jones
Journal:  Nucleic Acids Res       Date:  1997-06-15       Impact factor: 16.971

4.  COBRA: a sensitive and quantitative DNA methylation assay.

Authors:  Z Xiong; P W Laird
Journal:  Nucleic Acids Res       Date:  1997-06-15       Impact factor: 16.971

5.  Use of restriction enzymes to study eukaryotic DNA methylation: I. The methylation pattern in ribosomal DNA from Xenopus laevis.

Authors:  A P Bird; E M Southern
Journal:  J Mol Biol       Date:  1978-01-05       Impact factor: 5.469

Review 6.  Methylation matters.

Authors:  J F Costello; C Plass
Journal:  J Med Genet       Date:  2001-05       Impact factor: 6.318

  6 in total
  24 in total

Review 1.  Principles and challenges of genomewide DNA methylation analysis.

Authors:  Peter W Laird
Journal:  Nat Rev Genet       Date:  2010-03       Impact factor: 53.242

2.  Both hypomethylation and hypermethylation in a 0.2-kb region of a DNA repeat in cancer.

Authors:  Rie Nishiyama; Lixin Qi; Michelle Lacey; Melanie Ehrlich
Journal:  Mol Cancer Res       Date:  2005-11       Impact factor: 5.852

3.  Lymphocyte gene expression in subjects fed a low-choline diet differs between those who develop organ dysfunction and those who do not.

Authors:  Mihai D Niculescu; Kerry-Ann da Costa; Leslie M Fischer; Steven H Zeisel
Journal:  Am J Clin Nutr       Date:  2007-07       Impact factor: 7.045

4.  NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data.

Authors:  Michael Hackenberg; Guillermo Barturen; José L Oliver
Journal:  Nucleic Acids Res       Date:  2010-10-21       Impact factor: 16.971

5.  Event extraction for DNA methylation.

Authors:  Tomoko Ohta; Sampo Pyysalo; Makoto Miwa; Jun'ichi Tsujii
Journal:  J Biomed Semantics       Date:  2011-10-06

6.  DiseaseMeth: a human disease methylation database.

Authors:  Jie Lv; Hongbo Liu; Jianzhong Su; Xueting Wu; Hui Liu; Boyan Li; Xue Xiao; Fang Wang; Qiong Wu; Yan Zhang
Journal:  Nucleic Acids Res       Date:  2011-12-01       Impact factor: 16.971

Review 7.  From bytes to bedside: data integration and computational biology for translational cancer research.

Authors:  Jomol P Mathew; Barry S Taylor; Gary D Bader; Saiju Pyarajan; Marco Antoniotti; Arul M Chinnaiyan; Chris Sander; Steven J Burakoff; Bud Mishra
Journal:  PLoS Comput Biol       Date:  2007-02-23       Impact factor: 4.475

8.  PEpiD: a prostate epigenetic database in mammals.

Authors:  Jiejun Shi; Jian Hu; Qing Zhou; Yanhua Du; Cizhong Jiang
Journal:  PLoS One       Date:  2013-05-16       Impact factor: 3.240

9.  MethCancerDB--aberrant DNA methylation in human cancer.

Authors:  M Lauss; I Visne; A Weinhaeusel; K Vierlinger; C Noehammer; A Kriegner
Journal:  Br J Cancer       Date:  2008-02-05       Impact factor: 7.640

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

Authors:  Maté Ongenaert; Leander Van Neste; Tim De Meyer; Gerben Menschaert; Sofie Bekaert; Wim Van Criekinge
Journal:  Nucleic Acids Res       Date:  2007-10-11       Impact factor: 16.971

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