IMGT standardization for statistical analyses of T cell receptor junctions: The TRAV-TRAJ example

In Silico Biology

Volumn 6, Issue 6, 2006, Pages 573-588

  Bleakley, Kevin ^a   Giudicelli, Véronique ^b   Wu, Yan ^b   Lefranc, Marie Paule ^b,c   Biau, Gérard ^a  

^a UNIVERSITÉ DE MONTPELLIER   (France)

^b UMR 9002 CNRS UM   (France)

^c INSTITUT UNIVERSITAIRE DE FRANCE   (France)

Author keywords

Antibody; Classification; DNA rearrangement; IMGT; IMGT ONTOLOGY; IMGT JunctionAnalysis; IMGT V QUEST; Immunoglobulin; Joining gene; Junction; K Nearest Neighbors; Statistical learning; T cell receptor; TRAJ; TRAV; Variable gene

Indexed keywords

IMMUNOGLOBULIN; T LYMPHOCYTE RECEPTOR; LYMPHOCYTE ANTIGEN RECEPTOR;

ANALYTICAL ERROR; ARTICLE; AUTOMATION; COMPUTER PROGRAM; CONTROLLED STUDY; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; INTERNET; MATHEMATICAL ANALYSIS; PREDICTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SOMATIC MUTATION; STANDARDIZATION; STATISTICAL ANALYSIS; VDJ EXON; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MODEL; BIOLOGY; COMPLEMENTARITY DETERMINING REGION; GENETICS; GENOMICS; HUMAN; STANDARD; STATISTICS;

ARTIFICIAL INTELLIGENCE; COMPLEMENTARITY DETERMINING REGIONS; COMPUTATIONAL BIOLOGY; GENE REARRANGEMENT, T-LYMPHOCYTE; GENOMICS; HUMANS; MODELS, GENETIC; RECEPTORS, ANTIGEN, T-CELL; SOFTWARE;

EID: 34250618296     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (20)

1. Lefranc M.-P. and Lefranc. G, (2001). The T cell receptor FactsBook, Academic Press, London, UK, 398.
2. Lefranc M.-P. and Lefranc. G, (2001). The Immunoglobulin FactsBook, Academic Press, London, UK, 458.
3. Giudicelli. V. and Lefranc. M-P. (1999). Ontology for Immunogenetics: IMGT-ONTOLOGY. Bioinformatics 15 1047-1054.
4. Lefranc, M.-P., Giudicelli V., Ginestoux C., Bosc N., Folch G., Guiraudou D., Jabado-Michaloud J., Magris S., Scaviner D., Thouvenin V., Combres K., Girod D., Jeanjean S., Protat C., Yousfi-Monod M., Duprat E., Kaas Q., Pommié C., Chaume, D. and Lefranc, G. (2003). IMGT-ONTOLOGY for Immunogenetics and Immunoinformatics. In Silico Biol. 4, 0004.
5. Lefranc, M.-P., Clément, O., Kaas, Q., Duprat, E., Chastellan, P., Coelho, L., Combres, K., Ginestoux, C., Giudicelli, V., Chaunie, D. and Lefranc, G. (2004). IMGT-Choreography for Immunogenetics and Immunoinformatics. In Silico Biol. 5, 0006.
6. 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.
7. Giudicelli, V., Chaume, D., and Lefranc, M.-P. (2004). IMGT/V-QUEST, an integrated software for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis. Nucleic Acids Res. 32, W435-W440.
8. Yousfi Monod, M., Giudicelli, V., Chaume, D. and Lefranc, M.-P. (2004). IMGT/Junction Analysis: The first tool for the analysis of the immunoglobulin and T cell receptor complex V-J and V-D-J JUNCTIONs. Bioinformatics 20, i379-i385.
9. Landau, N. R., St. John, T. P., Weissman, I. L., Wolf, S. C., Silverstone, A. E. and Baltimore, D. (1984). Cloning of terminal transferase cDNA by antibody screening. Proc. Natl. Acad. Sci. USA 81 5 836-5840.
10. Lafaille, J. J., DeCloux, A., Bonneville, M., Takagaki, Y. and Tonegawa, S. (1989). Junctional sequences of T cell receptor γδ genes: implications for γδ T cell lineages and for a novel intermediate of V-(D)-J joining. Cell 59, 859-870.
11. Lewis, S. M. (1994). P nucleotide insertions and the resolution of hairpin DNA structures in mammalian cells. Proc. Natl. Acad. Sci. USA 91, 1332-1336.
12. Giudicelli, V., Duroux, P., Ginestoux, C., Folch, G., Jabado-Michaloud, J., Chaume, D. and Lefranc, M.-P. (2006). IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences. Nucleic Acids Res. 34, D781-D784.
13. Giudicelli, V., Chaume, D. and Lefranc, M.-P. (2005). IMGT/GENE-DB: A comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res. 33, D256-D261.
14. Chen, P. Y. (2002). Correlation: Parametric and nonparametric measures. Sage Publications, CA, USA.
15. Cover, T. M. and Thomas, J. A. (1991). Elements of Information Theory. John Wiley & Sons, New York, USA.
16. Boucheron, S., Bousquet, O. and Lugosi, G. (2005). Theory of classification: A survey of some recent advances. ESAIM: Probability and Statistics 9, 323-375.
17. Bousquet, O., Boucheron, S. and Lugosi, G. (2004). Introduction to statistical learning theory. In: Advanced Lectures in Machine Learning, Bousquet, O., Luxburg, U. V. and Räsch, G. (eds), Springer, New York, USA, pp. 169-207.
18. Devroye, L., Györfi, L. and Lugosi, G. (1996). A Probabilistic Theory of Pattern Recognition. Springer, New York, USA.
19. Duda, R. O., Hart, P, E. and Stork, D. G. (2000). Pattern Classification. Wiley Interscience, New York, USA.
20. Dasarathy, B. V. (1991). Nearest Neighbor (NN) Norms: NN Pattern Classification Techniques. IEEE CS Press, Los Alamitos, USA.