Baum Thierry-Pascal, Hierle Vivien, Pasqual Nicolas, Bellahcene Fatena, Chaume Denys, Lefranc Marie-Paule, Jouvin-Marche Evelyne, Marche Patrice Noël, Demongeot Jacques
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.
BMC Bioinformatics. 2006 Apr 26;7:224. doi: 10.1186/1471-2105-7-224.
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.
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.
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.
脊椎动物物种中的适应性免疫库多样性是由B淋巴细胞免疫球蛋白（IG）基因座以及T淋巴细胞T细胞受体（TR）基因座中的可变（V）、多样性（D）和连接（J）基因重组产生的。DNA水平上的这些V-J和V-D-J基因重排涉及重组信号序列（RSS）。尽管存在许多数据，但它们分散在具有不同命名法的非专业资源（如平面文件）中，难以提取。
IMGT/GeneInfo是一个在线信息系统，通过用户友好界面提供T细胞受体V-J和V-D-J重组复杂机制产生的详尽信息。T细胞包括分别表达αβ和γδ TR的两个群体。该系统的第一个版本处理了人类和小家鼠的TRA和TRB基因座，其基因重排允许合成αβ TR链。在本文中，我们展示了IMGT/GeneInfo的第二个版本，其中我们完善了人类和小家鼠TRG和TRD基因座的数据库，并引入了现有数据和新数据的质量控制程序。我们还为四个基因座分析添加了新功能，提供了一个非常有用的工具，可用于研究人类和小鼠物种所有TR基因座的V（D）J基因。IMGT/GeneInfo提供了超过59,000种重排组合，并带有完整的基因描述，可在http://imgt.cines.fr/GeneInfo免费获取。
IMGT/GeneInfo使所有TR信息序列集中在一处，现在只需在电脑上点击两下鼠标即可获取。这对生物学家和生物信息学家研究T淋巴细胞V（D）J基因重排及其在免疫反应分析中的应用很有用。
