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Volumn 7, Issue SEP, 2016, Pages

IMGT/statclonotype for pairwise evaluation and visualization of NGS IG and TR IMGT clonotype (AA) diversity or expression from IMGT/HighV-QUEST

Author keywords

Antibody; IMGT ONTOLOGY; IMGT HighV QUEST; Immunoglobulin; Immunoinformatics; Next generation sequencing; Statistical significance; T cell receptor

Indexed keywords

IMMUNOGLOBULIN; LYMPHOCYTE ANTIGEN RECEPTOR; T LYMPHOCYTE RECEPTOR;

EID: 84992130115     PISSN: None     EISSN: 16643224     Source Type: Journal    
DOI: 10.3389/fimmu.2016.00339     Document Type: Article
Times cited : (36)

References (36)
  • 4
    • 84895541683 scopus 로고    scopus 로고
    • ® and the birth and rise of immunoinformatics
    • ® and the birth and rise of immunoinformatics. Front Immunol (2014) 5:22. doi:10.3389/fimmu.2014.00022.
    • (2014) Front Immunol , vol.5 , pp. 22
    • Lefranc, M.-P.1
  • 5
    • 84867834056 scopus 로고    scopus 로고
    • ® web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing
    • ® web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. Immunome Res (2012) 8(1):2. doi:10.4172/1745-7580.1000056.
    • (2012) Immunome Res , vol.8 , Issue.1 , pp. 2
    • Alamyar, E.1    Giudicelli, V.2    Li, S.3    Duroux, P.4    Lefranc, M.-P.5
  • 6
    • 84867350002 scopus 로고    scopus 로고
    • ® tools for the nucleotide analysis of immunoglobulin IG and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS
    • ® tools for the nucleotide analysis of immunoglobulin IG and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. Methods Mol Biol (2012) 882:569-604. doi:10.1007/978-1-61779-842-9_32.
    • (2012) Methods Mol Biol , vol.882 , pp. 569-604
    • Alamyar, E.1    Duroux, P.2    Lefranc, M.-P.3    Giudicelli, V.4
  • 8
    • 84884165599 scopus 로고    scopus 로고
    • IMGT/HighV-QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling
    • Li S, Lefranc M-P, Miles JJ, Alamyar E, Giudicelli V, Duroux P, et al. IMGT/HighV-QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nat Commun (2013) 4:2333. doi:10.1038/ncomms3333.
    • (2013) Nat Commun , vol.4 , pp. 2333
    • Li, S.1    Lefranc, M.-P.2    Miles, J.J.3    Alamyar, E.4    Giudicelli, V.5    Duroux, P.6
  • 9
    • 84951304292 scopus 로고    scopus 로고
    • IMGT/HighV-QUEST statistical significance of IMGT clonotype (AA) diversity per gene for standardized comparisons of next generation sequencing immunoprofiles of immunoglobulins and T cell receptors
    • Aouinti S, Malouche D, Giudicelli V, Kossida S, Lefranc M-P. IMGT/HighV-QUEST statistical significance of IMGT clonotype (AA) diversity per gene for standardized comparisons of next generation sequencing immunoprofiles of immunoglobulins and T cell receptors. PLoS One (2015) 10(11):e0142353. doi:10.1371/journal.pone.0142353.
    • (2015) PLoS One , vol.10 , Issue.11
    • Aouinti, S.1    Malouche, D.2    Giudicelli, V.3    Kossida, S.4    Lefranc, M.-P.5
  • 12
    • 84897935016 scopus 로고    scopus 로고
    • Differences in the composition of the human antibody repertoire by B cell subsets in the blood
    • Mroczek ES, Ippolito GC, Rogosch T, Hoi KH, Hwangpo TA, Brand MG, et al. Differences in the composition of the human antibody repertoire by B cell subsets in the blood. Front Immunol (2014) 5:96. doi:10.3389/fimmu.2014.00096.
    • (2014) Front Immunol , vol.5 , pp. 96
    • Mroczek, E.S.1    Ippolito, G.C.2    Rogosch, T.3    Hoi, K.H.4    Hwangpo, T.A.5    Brand, M.G.6
  • 15
    • 84947402121 scopus 로고
    • Rectangular confidence regions for the means of multivariate normal distributions
    • Šidák Z. Rectangular confidence regions for the means of multivariate normal distributions. J Am Stat Assoc (1967) 62:626-33. doi:10.1080/01621459.1967.10482935.
    • (1967) J Am Stat Assoc , vol.62 , pp. 626-633
    • Šidák, Z.1
  • 16
    • 84992136405 scopus 로고
    • A simple sequentially rejective multiple test procedure
    • Holm S. A simple sequentially rejective multiple test procedure. Scand J Stat (1979) 6:65-70.
    • (1979) Scand J Stat , vol.6 , pp. 65-70
    • Holm, S.1
  • 17
    • 33645762226 scopus 로고
    • A sharper Bonferroni procedure for multiple tests of significance
    • Hochberg Y. A sharper Bonferroni procedure for multiple tests of significance. Biometrika (1988) 75(4):800-2. doi:10.1093/biomet/75.4.800.
    • (1988) Biometrika , vol.75 , Issue.4 , pp. 800-802
    • Hochberg, Y.1
  • 18
    • 84992096963 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Methodol (1995) 57(1):289-300. doi:10.2307/2346101.
    • (1995) J R Stat Soc Series B Methodol , vol.57 , Issue.1 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 19
    • 0035733108 scopus 로고    scopus 로고
    • The control of the false discovery rate in multiple testing under dependency
    • Benjamini Y, Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann Stat (2001) 29(4):1165-88. doi:10.1214/aos/1013699998.
    • (2001) Ann Stat , vol.29 , Issue.4 , pp. 1165-1188
    • Benjamini, Y.1    Yekutieli, D.2
  • 20
    • 13444273444 scopus 로고    scopus 로고
    • IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes
    • Giudicelli V, Chaume D, Lefranc M-P. IMGT/GENE-DB: a comprehensive database for human and mouse immunoglobulin and T cell receptor genes. Nucleic Acids Res (2005) 33:D256-61. doi:10.1093/nar/gki010.
    • (2005) Nucleic Acids Res , vol.33 , pp. D256-D261
    • Giudicelli, V.1    Chaume, D.2    Lefranc, M.-P.3
  • 21
    • 0037212339 scopus 로고    scopus 로고
    • IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains
    • Lefranc M-P, Pommié C, Ruiz M, Giudicelli V, Foulquier E, Truong L, et al. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol (2003) 27(1):55-77. doi:10.1016/S0145-305X(02)00039-3.
    • (2003) Dev Comp Immunol , vol.27 , Issue.1 , pp. 55-77
    • Lefranc, M.-P.1    Pommié, C.2    Ruiz, M.3    Giudicelli, V.4    Foulquier, E.5    Truong, L.6
  • 22
    • 1242276733 scopus 로고    scopus 로고
    • IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties
    • Pommié C, Levadoux S, Sabatier R, Lefranc G, Lefranc MP. IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties. J Mol Recognit (2004) 17:17-32. doi:10.1002/jmr.647.
    • (2004) J Mol Recognit , vol.17 , pp. 17-32
    • Pommié, C.1    Levadoux, S.2    Sabatier, R.3    Lefranc, G.4    Lefranc, M.P.5
  • 23
    • 84856043672 scopus 로고
    • The mathematical theory of communication
    • 423
    • Shannon CE. The mathematical theory of communication. Bell Syst Tech J (1948) 27(379-423):623-56. doi:10.1002/j.1538-7305.1948.tb00917.x.
    • (1948) Bell Syst Tech J , vol.27 , Issue.379 , pp. 623-656
    • Shannon, C.E.1
  • 24
    • 0017747498 scopus 로고
    • Unusual distribution of amino acids in complementarity-determing (hypervariable) segments of heavy and light chains of immunoglobulins and their possible roles in specificity of antibody combining sites
    • Kabat EA, Wu TT, Bilofsky H. Unusual distribution of amino acids in complementarity-determing (hypervariable) segments of heavy and light chains of immunoglobulins and their possible roles in specificity of antibody combining sites. J Biol Chem (1977) 252:6609-16.
    • (1977) J Biol Chem , vol.252 , pp. 6609-6616
    • Kabat, E.A.1    Wu, T.T.2    Bilofsky, H.3
  • 25
    • 33344464667 scopus 로고
    • Measurement of diversity
    • Simpson EH. Measurement of diversity. Nature (1949) 163:688. doi:10.1038/163688a0.
    • (1949) Nature , vol.163 , pp. 688
    • Simpson, E.H.1
  • 26
    • 84874137715 scopus 로고    scopus 로고
    • Immunoglobulin analysis tool: a novel tool for the analysis of human and mouse heavy and light chain transcripts
    • Rogosch T, Kerzel S, Hoi KH, Zhang Z, Maier RF, Ippolito GC, et al. Immunoglobulin analysis tool: a novel tool for the analysis of human and mouse heavy and light chain transcripts. Front Immunol (2012) 3:176. doi:10.3389/fimmu.2012.00176.
    • (2012) Front Immunol , vol.3 , pp. 176
    • Rogosch, T.1    Kerzel, S.2    Hoi, K.H.3    Zhang, Z.4    Maier, R.F.5    Ippolito, G.C.6
  • 28
    • 37249026668 scopus 로고    scopus 로고
    • Reshaping data with the reshape package
    • Wickham H. Reshaping data with the reshape package. J Stat Softw (2007) 21(12):1-20. doi:10.18637/jss.v021.i12.
    • (2007) J Stat Softw , vol.21 , Issue.12 , pp. 1-20
    • Wickham, H.1
  • 29
    • 84992044852 scopus 로고    scopus 로고
    • with contributions from Saporta R, Antonyan E. data.table: Extension of Data.frame. R Package Version 1.9.6
    • Dowle M, Srinivasan A, Short T, Lianoglou S, with contributions from Saporta R, Antonyan E. data.table: Extension of Data.frame. R Package Version 1.9.6. (2015). Available from: https://CRAN.R-project.org/package=data.table.
    • (2015)
    • Dowle, M.1    Srinivasan, A.2    Short, T.3    Lianoglou, S.4
  • 36
    • 33644922417 scopus 로고    scopus 로고
    • Multiple Testing Procedures: R multtest Package and Applications to Genomics
    • Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S, editors. New York: Springer (Statistics for Biology and Health Series)
    • Pollard KS, Dudoit S, van der Laan MJ. In: Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S, editors. Multiple Testing Procedures: R multtest Package and Applications to Genomics, in Bioinformatics and Computational Biology Solutions Using R and Bioconductor. New York: Springer (Statistics for Biology and Health Series) (2005).
    • (2005) Bioinformatics and Computational Biology Solutions Using R and Bioconductor
    • Pollard, K.S.1    Dudoit, S.2    van der Laan, M.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.