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IMGT/GENE-DB


NAR Molecular Biology Database Collection entry number 503
Giudicelli, V., Duroux, P., Ginestoux, C., Bellahcene, F., and Lefranc, M.-P.
Université Montpellier 2, CNRS, Montpellier, France.

Database Description

IMGT/GENE-DB is the IMGT® comprehensive genome database for immunoglobulins (IG) and T cell receptors (TR) genes from human and mouse, and, in developement, from other vertebrate species (e.g. rat). IMGT/GENE-DB is part of IMGT®, the international ImMunoGeneTics information system® (1,2), the high-quality integrated knowledge resource specialized in IG, TR, major histocompatibility complex (MHC) of human and other vertebrate species, and related proteins of the immune system (RPI) that belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT/GENE-DB annotated data are extracted from IMGT Repertoire, the global ImMunoGeneTics Web Resource, and from the IMGT/LIGM-DB database (3). All the human IMGT gene names (4,5) were approved by the Human Genome Organisation (HUGO) Nomenclature Committee (HGNC) in 1999 (6), and entered in the Genome DataBase GDB (Canada) and in LocusLink and Entrez Gene at NCBI (USA). IMGT/GENE-DB allows a search of IG and TR gene entries by locus, group, subgroup, based on the CLASSIFICATION axiom of IMGT-ONTOLOGY (7,8). A shortcut allows users to search genes by selection of gene name (according to the IMGT nomenclature) or clone name(s) (data from the "Reference sequences" and "Sequences from the literature" columns in IMGT Repertoire>Germline genes tables). IMGT/GENE-DB entries provide, for each gene, the chromosomal localization, the gene name and definition, the number of alleles, links to IMGT Repertoire and to external sequence (EMBL, GenBank, DDBJ) and genome (e.g., GDB, Entrez Gene, OMIM) databases. IMGT/GENE-DB provides for each allele the functionality, the clone names, the IMGT/LIGM-DB reference sequence accession numbers (with link to the flat file), and the "IMGT/GENE-DB reference sequences in FASTA format" (nucleotide and amino acid sequences of the coding regions extracted from the IMGT/LIGM-DB reference sequence), with gaps according to the IMGT unique numbering (9,10) (based on the IMGT Scientific chart rules and on the NUMEROTATION axiom of IMGT-ONTOLOGY). IMGT/GENE-DB was implemented by Véronique Giudicelli, and has been available on the Web since February 2003.

Recent Developments

In April 2008, IMGT/GENE-DB contained 1,900 genes and 2,894 alleles (673 IG and TR genes and 1,233 alleles from Homo sapiens, 832 IG and TR genes and 1,264 alleles from Mus musculus, Mus cookii, Mus pahari, Mus spretus, Mus saxicola, Mus minutoides, and 395 IGH genes and 397 alleles from Rattus norvegicus).

Acknowledgements

IMGT® received funding from the European Union (EU) programmes BIOMED1 (BIOCT930038), BIOTECH2 (BIO4CT960037), 5th PCRDT (QLG2-2000-01287) and 6th PCRDT (ImmunoGrid IST-028069), from the Agence Nationale de la Recherche ANR (BIOSYS06-135457) and from the Région Languedoc-Roussillon. IMGT® is funded by the Centre National de la Recherche Scientifique (CNRS), the Ministère de l'Education Nationale and the Ministère de la Recherche.

References

1. Lefranc, M.-P., Giudicelli, V., Kaas, Q., Duprat, E., Jabado-Michaloud, J., Scaviner, D., Ginestoux, C., Clément, O., Chaume, D., and Lefranc, G. (2005) IMGT, the international ImMunoGeneTics information system®. Nucleic Acids Res., 33, D593-D597.
2. Lefranc M.-P., Clément O., Kaas Q., Duprat E., Chastellan P., Coelho I., Combres K., Ginestoux C., Giudicelli V., Chaume D. and Lefranc G., IMGT-Choreography for Immunogenetics and Immunoinformatics, In Silico Biology, 2005, 5, 45-60. Epub 5 0006 24 December 2004 http://www.bioinfo.de/isb/2004/05/0006/,PMID:15972004
3. Giudicelli V., Ginestoux C., Folch G., Jabado-Michaloud J., Chaume D. and Lefranc, M.-P. IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences, Nucleic Acids Res., 2006, 34, D781-D784, PMID:16381979
4. Lefranc M.-P. and Lefranc G., The Immunoglobulin FactsBook, Academic Press, 458 pages, 2001, ISBN:012441351X
5. Lefranc M.-P. and Lefranc G., The T cell receptor FactsBook, Academic Press, 398 pages, 2001, ISBN:0124413528
6. Wain, H.M., Bruford E.A., Lovering R.C., Lush M.J., Wright M.W. and Povey S., Guidelines for human gene nomenclature, Genomics, 2002, 79, 464-470, PMID:11944974
7. Giudicelli, V. and Lefranc, M.-P. Ontology for immunogenetics: the IMGT-ONTOLOGY, Bioinformatics, 1999, 15, 1047-1054, PMID:10745995
8. Duroux P., Kaas Q., Brochet X., Lane J., Ginestoux C., Lefranc M.-P. and Giudicelli V., IMGT-Kaleidoscope, the Formal IMGT-ONTOLOGY paradigm, Biochimie, 2008, 90, 570-583, PMID:17949886
9. Lefranc M.-P., Pommié C., Ruiz M., Giudicelli V., Foulquier E., Truong L., Thouvenin-Contet V. and Lefranc G., IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev. Comp. Immunol., 2003, 27, 55-77, PMID:12477501
10. Lefranc M.-P., Pommié C., Kaas Q., Duprat E., Bosc N., Guiraudou D., Jean C., Ruiz M., Da Piedade I., Rouard M., Foulquier E., Thouvenin V. and Lefranc G., IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains, Dev. Comp. Immunol., 2005, 29, 185-203, PMID:15572068


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