The MethDB DAS Server Adding an Epigenetic Information Layer to the Human Genome

被引：15

作者：

Negre, Vincent ^{[1
]}

Grunau, Christoph ^{[1
]}

机构：

[1] CNRS, UPR 1142, Inst Genet Humaine, F-34396 Montpellier, France

来源：

EPIGENETICS | 2006年 / 1卷 / 02期

关键词：

biological database; distributed annotation system; DNA methylation; human genome;

D O I：

10.4161/epi.1.2.2765

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The DNA methylation database MethDB (www.methdb.net) was developed in order to standardize and collect the dispersed data about this epigenetic phenomenon in a common resource. In the first version of MethDB, data was gathered by annotators and the database could only be queried. In a second step, we added an on-line data submission system that is open to the public. Here we present the DAS annotation server of MethDB that allows integration of MethDB into the network of biological databases via the Distributed Annotation System (DAS) and the representation of DNA methylation data as an epigenetic information layer to the human genome. In order to validate our system and to incorporate the data of the first large scale methylation analysis of the human genome, we assembled the 31312 sequences of the human CpG island tagging project into 13786 CpG islands and imported them into MethDB. The database contains now 19905 methylation content data and 5382 methylation patterns or profiles for 48 species, 1511 individuals, 198 tissues and cell lines and 79 phenotypes.

引用

页码：101 / 105

页数：5

共 7 条

[1] Prediction of methylated CpGs in DNA sequences using a support vector machine [J].

Bhasin, M ;

Zhang, H ;

Reinherz, EL ;

Reche, PA .

FEBS LETTERS, 2005, 579 (20) :4302-4308

[2] PURIFICATION OF CPG ISLANDS USING A METHYLATED DNA-BINDING COLUMN [J].

CROSS, SH ;

CHARLTON, JA ;

NAN, XS ;

BIRD, AP .

NATURE GENETICS, 1994, 6 (03) :236-244

[3] The Distributed Annotation System [J].

Dowell, Robin D. ;

Jokerst, Rodney M. ;

Day, Allen ;

Eddy, Sean R. ;

Stein, Lincoln .

BMC BIOINFORMATICS, 2001, 2 (1)

[4] Ensembl 2005 [J].

Hubbard, T ;

Andrews, D ;

Caccamo, M ;

Cameron, G ;

Chen, Y ;

Clamp, M ;

Clarke, L ;

Coates, G ;

Cox, T ;

Cunningham, F ;

Curwen, V ;

Cutts, T ;

Down, T ;

Durbin, R ;

Fernandez-Suarez, XM ;

Gilbert, J ;

Hammond, M ;

Herrero, J ;

Hotz, H ;

Howe, K ;

Iyer, V ;

Jekosch, K ;

Kahari, A ;

Kasprzyk, A ;

Keefe, D ;

Keenan, S ;

Kokocinsci, F ;

London, D ;

Longden, I ;

McVicker, G ;

Melsopp, C ;

Meidl, P ;

Potter, S ;

Proctor, G ;

Rae, M ;

Rios, D ;

Schuster, M ;

Searle, S ;

Severin, J ;

Slater, G ;

Smedley, D ;

Smith, J ;

Spooner, W ;

Stabenau, A ;

Stalker, J ;

Storey, R ;

Trevanion, S ;

Ureta-Vidal, A ;

Vogel, J ;

White, S .

NUCLEIC ACIDS RESEARCH, 2005, 33 :D447-D453

[5] Cyclin D1 gene activation in human myeloma cells is independent of DNA hypomethylation or histone hyperacetylation [J].

Krieger, S ;

Grunau, C ;

Sabbah, M ;

Sola, B .

EXPERIMENTAL HEMATOLOGY, 2005, 33 (06) :652-659

[6] eL-DASionator: an LDAS upload file generator [J].

Negre, V ;

Grunau, C .

BMC BIOINFORMATICS, 2004, 5 (1)

[7]

Staden R, 2000, Methods Mol Biol, V132, P115

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