메뉴 건너뛰기




Volumn 182, Issue 10, 2009, Pages 6011-6021

A network modeling approach to analysis of the Th2 memory responses underlying human atopic disease

Author keywords

[No Author keywords available]

Indexed keywords

DIPEPTIDYL PEPTIDASE IV; INTERLEUKIN 13; INTERLEUKIN 2 RECEPTOR; INTERLEUKIN 4 RECEPTOR; INTERLEUKIN 5; TRANSCRIPTION FACTOR FOXP3;

EID: 77649252969     PISSN: 00221767     EISSN: 15506606     Source Type: Journal    
DOI: 10.4049/jimmunol.0804125     Document Type: Article
Times cited : (30)

References (68)
  • 1
    • 27844446240 scopus 로고    scopus 로고
    • Embracing complexity, inching closer to reality
    • 2005
    • Schadt, E. E., A. Sachs, and S. Friend. 2005. Embracing complexity, inching closer to reality. Sci. STKE 2005: pe40.
    • (2005) Sci. STKE
    • Schadt, E.E.1    Sachs, A.2    Friend, S.3
  • 2
    • 10044298236 scopus 로고    scopus 로고
    • Reductionism and complexity in molecular biology: Scientists now have the tools to unravel biological and overcome the limitations of reductionism
    • Van Regenmortel, M. H. 2004. Reductionism and complexity in molecular biology: scientists now have the tools to unravel biological and overcome the limitations of reductionism. EMBO Rep. 5: 1016-1020.
    • (2004) EMBO Rep. , vol.5 , pp. 1016-1020
    • Van Regenmortel, M.H.1
  • 3
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabasi, A. L., and Z. N. Oltvai. 2004. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5: 101-113.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 4
    • 7644238181 scopus 로고    scopus 로고
    • Biological robustness
    • Kitano, H. 2004. Biological robustness. Nat. Rev. Genet. 5: 826-837.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 826-837
    • Kitano, H.1
  • 6
    • 0042154192 scopus 로고    scopus 로고
    • Evolutionary capacitance as a general feature of complex gene networks
    • DOI 10.1038/nature01765
    • Bergman, A., and M. L. Siegal. 2003. Evolutionary capacitance as a general feature of complex gene networks. Nature 424: 549-552. (Pubitemid 36975775)
    • (2003) Nature , vol.424 , Issue.6948 , pp. 549-552
    • Bergman, A.1    Siegal, M.L.2
  • 7
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • Luscombe, N. M., M. M. Babu, H. Yu, M. Snyder, S. A. Teichmann, and M. Gerstein. 2004. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308-312.
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.M.1    Babu, M.M.2    Yu, H.3    Snyder, M.4    Teichmann, S.A.5    Gerstein, M.6
  • 8
    • 0034721164 scopus 로고    scopus 로고
    • Error and attack tolerance of complex networks
    • DOI 10.1038/35019019
    • Albert, R., H. Jeong, and A. L. Barabasi. 2000. Error and attack tolerance of complex networks. Nature 406: 378-382. (Pubitemid 30625551)
    • (2000) Nature , vol.406 , Issue.6794 , pp. 378-382
    • Albert, R.1    Jeong, H.2    Barabasi, A.-L.3
  • 10
    • 33645221650 scopus 로고    scopus 로고
    • Gene connectivity, function, and sequence conservation: Predictions from modular yeast co-expression networks
    • Carlson, M. R., B. Zhang, Z. Fang, P. S. Mischel, S. Horvath, and S. F. Nelson. 2006. Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics 7: 40.
    • (2006) BMC Genomics , vol.7 , pp. 40
    • Carlson, M.R.1    Zhang, B.2    Fang, Z.3    Mischel, P.S.4    Horvath, S.5    Nelson, S.F.6
  • 11
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong, H., S. P. Mason, A. L. Barabasi, and Z. N. Oltvai. 2001. Lethality and centrality in protein networks. Nature 411: 41-42.
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.L.3    Oltvai, Z.N.4
  • 12
    • 38649138295 scopus 로고    scopus 로고
    • A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans
    • DOI 10.1038/ng.2007.70, PII NG200770
    • Lee, I., B. Lehner, C. Crombie, W. Wong, A. G. Fraser, and E. M. Marcotte. 2008. A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat. Genet. 40: 181-188. (Pubitemid 351171397)
    • (2008) Nature Genetics , vol.40 , Issue.2 , pp. 181-188
    • Lee, I.1    Lehner, B.2    Crombie, C.3    Wong, W.4    Fraser, A.G.5    Marcotte, E.M.6
  • 13
  • 15
    • 33645276014 scopus 로고    scopus 로고
    • A plaidoyer for "systems immunology"
    • Benoist, C., R. N. Germain, and D. Mathis. 2006. A plaidoyer for "systems immunology". Immunol. Rev. 210: 229-234.
    • (2006) Immunol. Rev. , vol.210 , pp. 229-234
    • Benoist, C.1    Germain, R.N.2    Mathis, D.3
  • 16
    • 33645786050 scopus 로고    scopus 로고
    • Identification of novel Th2-associated genes in T memory responses to allergens
    • Bosco, A., K. L. McKenna, C. J. Devitt, M. J. Firth, P. D. Sly, and P. G. Holt. 2006. Identification of novel Th2-associated genes in T memory responses to allergens. J. Immunol. 176: 4766-4777.
    • (2006) J. Immunol. , vol.176 , pp. 4766-4777
    • Bosco, A.1    McKenna, K.L.2    Devitt, C.J.3    Firth, M.J.4    Sly, P.D.5    Holt, P.G.6
  • 18
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • article 3
    • Smyth, G. K. 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3: article 3.
    • (2004) Stat. Appl. Genet. Mol. Biol. , vol.3
    • Smyth, G.K.1
  • 19
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini, Y., and Y. Hochberg. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57: 289-300.
    • (1995) J. R. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 20
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher, V. G., R. Tibshirani, and G. Chu. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98: 5116-5121.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 21
    • 0037276175 scopus 로고    scopus 로고
    • Statistical tests for differential expression in cDNA microarray experiments
    • Cui, X., and G. A. Churchill. 2003. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol. 4: 210.
    • (2003) Genome Biol. , vol.4 , pp. 210
    • Cui, X.1    Churchill, G.A.2
  • 22
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • DOI 10.1126/science.1073374
    • Ravasz, E., A. L. Somera, D. A. Mongru, Z. N. Oltvai, and A. L. Barabasi. 2002. Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555. (Pubitemid 34971002)
    • (2002) Science , vol.297 , Issue.5586 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3    Oltvai, Z.N.4    Barabasi, A.-L.5
  • 23
    • 40049099114 scopus 로고    scopus 로고
    • Defining clusters from a hierarchical cluster tree: The Dynamic Tree Cut package for R
    • DOI 10.1093/bioinformatics/btm563
    • Langfelder, P., B. Zhang, and S. Horvath. 2008. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut library for R. Bioinformatics 24: 719-720. (Pubitemid 351321220)
    • (2008) Bioinformatics , vol.24 , Issue.5 , pp. 719-720
    • Langfelder, P.1    Zhang, B.2    Horvath, S.3
  • 24
    • 35348890683 scopus 로고    scopus 로고
    • On testing the significance of sets of genes
    • Efron, B., and R. Tibshirani. 2007. On testing the significance of sets of genes. Ann. Appl. Stat. 1: 107-109.
    • (2007) Ann. Appl. Stat. , vol.1 , pp. 107-109
    • Efron, B.1    Tibshirani, R.2
  • 25
    • 0035733108 scopus 로고    scopus 로고
    • The control of the false discovery rate in multiple testing under dependency
    • DOI 10.1214/aos/1013699998
    • Benjamini, Y., and D. Yekutieli. 2001. The control of the false discovery rate in multiple testing under dependency. Ann Stat. 29: 1165-1188. (Pubitemid 33575263)
    • (2001) Annals of Statistics , vol.29 , Issue.4 , pp. 1165-1188
    • Benjamini, Y.1    Yekutieli, D.2
  • 26
    • 33747019547 scopus 로고    scopus 로고
    • Centering, scaling, and transformations: Improving the biological information content of metabolomics data
    • van den Berg, R. A., H. C. Hoefsloot, J. A. Westerhuis, A. K. Smilde, and M. J. van der Werf. 2006. Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC Genomics 7: 142.
    • (2006) BMC Genomics , vol.7 , pp. 142
    • Van Den Berg, R.A.1    Hoefsloot, H.C.2    Westerhuis, J.A.3    Smilde, A.K.4    Van Der Werf, M.J.5
  • 27
    • 35448966105 scopus 로고    scopus 로고
    • Human regulatory T cells: A unique, stable thymic subset or a reversible peripheral state of differentiation?
    • DOI 10.1016/j.imlet.2007.08.012, PII S0165247807002039
    • Pillai, V., and N. J. Karandikar. 2007. Human regulatory T cells: a unique, stable thymic subset or a reversible peripheral state of differentiation? Immunol. Lett. 114: 9-15. (Pubitemid 47625594)
    • (2007) Immunology Letters , vol.114 , Issue.1 , pp. 9-15
    • Pillai, V.1    Karandikar, N.J.2
  • 29
    • 33845569346 scopus 로고    scopus 로고
    • Thematic review series: Systems biology approaches to metabolic and cardiovascular disorders: reverse engineering gene networks to identify key drivers of complex disease phenotypes
    • Schadt, E. E., and P. Y. Lum. 2006. Thematic review series: systems biology approaches to metabolic and cardiovascular disorders: reverse engineering gene networks to identify key drivers of complex disease phenotypes. J. Lipid Res. 47: 2601-2613.
    • (2006) J. Lipid Res. , vol.47 , pp. 2601-2613
    • Schadt, E.E.1    Lum, P.Y.2
  • 30
    • 36048978911 scopus 로고    scopus 로고
    • Foxp3 transcription-factor-dependent and -independent regulation of the regulatory T cell transcriptional signature
    • Hill, J. A., M. Feuerer, K. Tash, S. Haxhinasto, J. Perez, R. Melamed, D. Mathis, and C. Benoist. 2007. Foxp3 transcription-factor-dependent and -independent regulation of the regulatory T cell transcriptional signature. Immunity 27: 786-800.
    • (2007) Immunity , vol.27 , pp. 786-800
    • Hill, J.A.1    Feuerer, M.2    Tash, K.3    Haxhinasto, S.4    Perez, J.5    Melamed, R.6    Mathis, D.7    Benoist, C.8
  • 33
    • 23144466889 scopus 로고    scopus 로고
    • VisANT: Data-integrating visual framework for biological networks and modules
    • Hu, Z., J. Mellor, J. Wu, T. Yamada, D. Holloway, and C. Delisi. 2005. VisANT: data-integrating visual framework for biological networks and modules. Nucleic Acids Res. 33: W352-W357.
    • (2005) Nucleic Acids Res. , vol.33
    • Hu, Z.1    Mellor, J.2    Wu, J.3    Yamada, T.4    Holloway, D.5    Delisi, C.6
  • 34
    • 0025082313 scopus 로고
    • Generation of interleukin 4 (IL-4)-producing cells in vivo and in vitro: IL-2 and IL-4 are required for in vitro generation of IL-4-producing cells
    • DOI 10.1084/jem.172.3.921
    • Le Gros, G., S. Z. Ben-Sasson, R. Seder, F. D. Finkelman, and W. E. Paul. 1990. Generation of interleukin 4 (IL-4)-producing cells in vivo and in vitro: IL-2 and IL-4 are required for in vitro generation of IL-4-producing cells. J. Exp. Med. 172: 921-929. (Pubitemid 20301238)
    • (1990) Journal of Experimental Medicine , vol.172 , Issue.3 , pp. 921-929
    • Le Gros, G.1    Ben-Sasson, S.Z.2    Seder, R.3    Finkelman, F.D.4    Paul, W.E.5
  • 35
    • 0025222698 scopus 로고
    • IL-4 directs the development of Th2-like helper effectors
    • Swain, S. L., A. D. Weinberg, M. English, and G. Huston. 1990. IL-4 directs the development of Th2-like helper effectors. J. Immunol. 145: 3796-3806.
    • (1990) J. Immunol. , vol.145 , pp. 3796-3806
    • Swain, S.L.1    Weinberg, A.D.2    English, M.3    Huston, G.4
  • 36
    • 0033554726 scopus 로고    scopus 로고
    • Two subsets of memory T lymphocytes with distinct homing potentials and effector functions
    • Sallusto, F., D. Lenig, R. Forster, M. Lipp, and A. Lanzavecchia. 1999. Two subsets of memory T lymphocytes with distinct homing potentials and effector functions. Nature 401: 708-712. (Pubitemid 129515761)
    • (1999) Nature , vol.401 , Issue.6754 , pp. 708-712
    • Sallusto, F.1    Lenig, D.2    Forster, R.3    Lipp, M.4    Lanzavecchia, A.5
  • 37
    • 33745091465 scopus 로고    scopus 로고
    • Functional signatures of protective antiviral T-cell immunity in human virus infections
    • DOI 10.1111/j.0105-2896.2006.00395.x
    • Harari, A., V. Dutoit, C. Cellerai, P. A. Bart, R. A. Du Pasquier, and G. Pantaleo. 2006. Functional signatures of protective antiviral T-cell immunity in human virus infections. Immunol. Rev. 211: 236-254. (Pubitemid 43882976)
    • (2006) Immunological Reviews , vol.211 , pp. 236-254
    • Harari, A.1    Dutoit, V.2    Cellerai, C.3    Bart, P.-A.4    Du Pasquier, R.A.5    Pantaleo, G.6
  • 38
    • 27744494860 scopus 로고    scopus 로고
    • Stepwise differentiation of CD4 memory T cells defined by expression of CCR7 and CD27
    • Fritsch, R. D., X. Shen, G. P. Sims, K. S. Hathcock, R. J. Hodes, and P. E. Lipsky. 2005. Stepwise differentiation of CD4 memory T cells defined by expression of CCR7 and CD27. J. Immunol. 175: 6489-6497.
    • (2005) J. Immunol. , vol.175 , pp. 6489-6497
    • Fritsch, R.D.1    Shen, X.2    Sims, G.P.3    Hathcock, K.S.4    Hodes, R.J.5    Lipsky, P.E.6
  • 41
    • 35448930435 scopus 로고    scopus 로고
    • +FOXP3 T cells by T-cell receptor stimulation is transforming growth factor-β dependent but does not confer a regulatory phenotype
    • +FOXP3 T cells by T-cell receptor stimulation is transforming growth factor-β dependent but does not confer a regulatory phenotype. Blood 110: 2983-2990.
    • (2007) Blood , vol.110 , pp. 2983-2990
    • Tran, D.Q.1    Ramsey, H.2    Shevach, E.M.3
  • 43
    • 33847125247 scopus 로고    scopus 로고
    • Regulatory T-cell functions are subverted and converted owing to attenuated Foxp3 expression
    • Wan, Y. Y., and R. A. Flavell. 2007. Regulatory T-cell functions are subverted and converted owing to attenuated Foxp3 expression. Nature 445: 766-770.
    • (2007) Nature , vol.445 , pp. 766-770
    • Wan, Y.Y.1    Flavell, R.A.2
  • 44
    • 38049110724 scopus 로고    scopus 로고
    • Attack on the clones?: Human FOXP3 detection by PCH101, 236A/E7, 206D, and 259D reveals 259D as the outlier with lower sensitivity
    • author reply 464-466
    • Pillai, V., and N. J. Karandikar. 2008. Attack on the clones?: human FOXP3 detection by PCH101, 236A/E7, 206D, and 259D reveals 259D as the outlier with lower sensitivity. Blood 111: 463-464; author reply 464-466.
    • (2008) Blood , vol.111 , pp. 463-464
    • Pillai, V.1    Karandikar, N.J.2
  • 45
    • 27944455288 scopus 로고    scopus 로고
    • Sequential development of interleukin 2-dependent effector and regulatory T cells in response to endogenous systemic antigen
    • DOI 10.1084/jem.20050855
    • Knoechel, B., J. Lohr, E. Kahn, J. A. Bluestone, and A. K. Abbas. 2005. Sequential development of interleukin 2-dependent effector and regulatory T cells in response to endogenous systemic antigen. J. Exp. Med. 202: 1375-1386. (Pubitemid 41668740)
    • (2005) Journal of Experimental Medicine , vol.202 , Issue.10 , pp. 1375-1386
    • Knoechel, B.1    Lohr, J.2    Kahn, E.3    Bluestone, J.A.4    Abbas, A.K.5
  • 51
    • 47249134183 scopus 로고    scopus 로고
    • Plasticity of regulatory T cells: Subversion of suppressive function and conversion to enhancement of lung allergic responses
    • Joetham, A., S. Matsubara, M. Okamoto, K. Takeda, N. Miyahara, A. Dakhama, and E. W. Gelfand. 2008. Plasticity of regulatory T cells: subversion of suppressive function and conversion to enhancement of lung allergic responses. J. Immunol. 180: 7117-7124.
    • (2008) J. Immunol. , vol.180 , pp. 7117-7124
    • Joetham, A.1    Matsubara, S.2    Okamoto, M.3    Takeda, K.4    Miyahara, N.5    Dakhama, A.6    Gelfand, E.W.7
  • 55
    • 39449133957 scopus 로고    scopus 로고
    • A mechanism for the initiation of allergen-induced T helper type 2 responses
    • Sokol, C. L., G. M. Barton, A. G. Farr, and R. Medzhitov. 2008. A mechanism for the initiation of allergen-induced T helper type 2 responses. Nat. Immunol. 9: 310-318.
    • (2008) Nat. Immunol. , vol.9 , pp. 310-318
    • Sokol, C.L.1    Barton, G.M.2    Farr, A.G.3    Medzhitov, R.4
  • 56
    • 1642306579 scopus 로고    scopus 로고
    • IL-4-dependent Th2 collateral priming to inhaled antigens independent of Toll-like receptor 4 and myeloid differentiation factor 88
    • Eisenbarth, S. C., A. Zhadkevich, P. Ranney, C. A. Herrick, and K. Bottomly. 2004. IL-4-dependent Th2 collateral priming to inhaled antigens independent of Toll-like receptor 4 and myeloid differentiation factor 88. J. Immunol. 172: 4527-4534.
    • (2004) J. Immunol. , vol.172 , pp. 4527-4534
    • Eisenbarth, S.C.1    Zhadkevich, A.2    Ranney, P.3    Herrick, C.A.4    Bottomly, K.5
  • 57
    • 40049092917 scopus 로고    scopus 로고
    • Treatment strategies for allergy and asthma
    • Holgate, S. T., and R. Polosa. 2008. Treatment strategies for allergy and asthma. Nat. Rev. Immunol. 8: 218-230.
    • (2008) Nat. Rev. Immunol. , vol.8 , pp. 218-230
    • Holgate, S.T.1    Polosa, R.2
  • 60
    • 17044421246 scopus 로고    scopus 로고
    • Recent findings on genes associated with inflammatory disease
    • DOI 10.1016/j.mrfmmm.2004.06.061, Single Nucleotide Polymorphisms (SNPs): Detection, Interpretation, and Applications
    • Yamada, R., and K. Ymamoto. 2005. Recent findings on genes associated with inflammatory disease. Mutat. Res. 573: 136-151. (Pubitemid 40501976)
    • (2005) Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis , vol.573 , Issue.1-2 , pp. 136-151
    • Yamada, R.1    Ymamoto, K.2
  • 61
    • 0028784289 scopus 로고
    • Interleukin-2 receptor alpha chain regulates the size and content of the peripheral lymphoid compartment
    • Willerford, D. M., J. Chen, J. A. Ferry, L. Davidson, A. Ma, and F. W. Alt. 1995. Interleukin-2 receptor alpha chain regulates the size and content of the peripheral lymphoid compartment. Immunity 3: 521-530.
    • (1995) Immunity , vol.3 , pp. 521-530
    • Willerford, D.M.1    Chen, J.2    Ferry, J.A.3    Davidson, L.4    Ma, A.5    Alt, F.W.6
  • 64
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: A brief overview
    • Kitano, H. 2002. Systems biology: a brief overview. Science 295: 1662-1664.
    • (2002) Science , vol.295 , pp. 1662-1664
    • Kitano, H.1
  • 66
    • 54249155522 scopus 로고    scopus 로고
    • Network pharmacology: The next paradigm in drug discovery
    • Hopkins, A. L. 2008. Network pharmacology: the next paradigm in drug discovery. Nat. Chem. Biol. 4: 682-690.
    • (2008) Nat. Chem. Biol. , vol.4 , pp. 682-690
    • Hopkins, A.L.1
  • 67
    • 30744466671 scopus 로고    scopus 로고
    • The role of T lymphocytes in asthma
    • Kay, A. 2006. The role of T lymphocytes in asthma. Chem. Immunol. Allergy 91: 59-75.
    • (2006) Chem. Immunol. Allergy , vol.91 , pp. 59-75
    • Kay, A.1
  • 68
    • 0035577641 scopus 로고    scopus 로고
    • Identification and validation of endogenous reference genes for expression profiling of T helper cell differentiation by quantitative real-time RT-PCR
    • Hamalainen, H. K., J. C. Tubman, S. Vikman, T. Kyrola, E. Ylikoski, J. A. Warrington, and R. Lahesmaa. 2001. Identification and validation of endogenous reference genes for expression profiling of T helper cell differentiation by quantitative real-time RT-PCR. Anal. Biochem. 299: 63-70.
    • (2001) Anal. Biochem. , vol.299 , pp. 63-70
    • Hamalainen, H.K.1    Tubman, J.C.2    Vikman, S.3    Kyrola, T.4    Ylikoski, E.5    Warrington, J.A.6    Lahesmaa, R.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.