IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations.
BACKGROUND
Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V), diversity (D) and joining (J) genes in the immunoglobulin (IG) loci of B lymphocytes and in the T cell receptor (TR) loci of T lymphocytes. These V-J and V-D-J gene rearrangements at the DNA level involve recombination signal sequences (RSS). Whereas many data exist, they are scattered in non specialized resources with different nomenclatures (eg. flat files) and are difficult to extract.


METHODS
IMGT/GeneInfo is an online information system that provides, through a user-friendly interface, exhaustive information resulting from the complex mechanisms of T cell receptor V-J and V-D-J recombinations. T cells comprise two populations which express the alphabeta and gammadelta TR, respectively. The first version of the system dealt with the Homo sapiens and Mus musculus TRA and TRB loci whose gene rearrangements allow the synthesis of the alphabeta TR chains. In this paper, we present the second version of IMGT/GeneInfo where we complete the database for the Homo sapiens and Mus musculus TRG and TRD loci along with the introduction of a quality control procedure for existing and new data. We also include new functionalities to the four loci analysis, giving, to date, a very informative tool which allows to work on V(D)J genes of all TR loci in both human and mouse species. IMGT/GeneInfo provides more than 59,000 rearrangement combinations with a full gene description which is freely available at http://imgt.cines.fr/GeneInfo.


CONCLUSIONS
IMGT/GeneInfo allows all TR information sequences to be in the same spot, and are now available within two computer-mouse clicks. This is useful for biologists and bioinformaticians for the study of T lymphocyte V(D)J gene rearrangements and their applications in immune response analysis.
Baum
Thierry-Pascal
TP
Laboratoire TIMC-IMAG-CNRS UMR 5525, Techniques de l'Imagerie, de la Modélisation et de la Cognition, Université Joseph Fourier, Grenoble 1, Faculté de Médecine, Domaine de la Merci, 38706 La Tronche, France. tpbaum@imag.fr
Hierle
Vivien
V
Pasqual
Nicolas
N
Bellahcene
Fatena
F
Chaume
Denys
D
Lefranc
Marie-Paule
MP
Jouvin-Marche
Evelyne
E
Marche
Patrice Noël
PN
Demongeot
Jacques
J
D000818:Animals; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D015321:Gene Rearrangement / Q000235:genetics*; D005803:Genes, Immunoglobulin / Q000235:genetics; D019676:Genes, T-Cell Receptor delta / Q000235:genetics*; D019675:Genes, T-Cell Receptor gamma / Q000235:genetics*; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D051379:Mice; D011948:Receptors, Antigen, T-Cell / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics
D011948:Receptors, Antigen, T-Cell