A protein interaction network associated with asthma

Journal of Theoretical Biology

Volumn 252, Issue 4, 2008, Pages 722-731

  Hwang, Sohyun ^a,b   Son, Seung Woo ^a   Kim, Sang Cheol ^b,c   Kim, Young Joo ^b   Jeong, Hawoong ^a   Lee, Doheon ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^c Yonsei University   (South Korea)

Author keywords

Disease network; Microarray expression; Protein protein interaction; System biology

Indexed keywords

ASTHMA; DISEASE; GENE; MAPPING; PROTEIN;

ARTICLE; ASTHMA; BIOLOGICAL ACTIVITY; CBL GENE; CELL FUNCTION; DRUG TARGETING; GENE MUTATION; GENE TARGETING; GENETIC ANALYSIS; GNB2L1 GENE; HUMAN; ONCOGENE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; VAV1 GENE;

ASTHMA; CELL PHYSIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; SYSTEMS BIOLOGY;

EID: 44449119819     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2008.02.011     Document Type: Article

References (70)

1. Adachi T., Cui C.H., Kanda A., Kayaba H., Ohta K., and Chihara J. Activation of epidermal growth factor receptor via CCR3 in bronchial epithelial cells. Biochem. Biophys. Res. Commun. 320 (2004) 292-296
2. Albert R., Jeong H., and Barabasi A.L. Error and attack tolerance of complex networks. Nature 406 (2000) 378-382
3. Alberts B., Johnson A., Lewis J., Raff M., Roberts K., and Walter P. Molecular Biology of the Cell (2002), Garland Science
4. Amrani Y., Chen H., and Panettieri Jr. R.A. Activation of tumor necrosis factor receptor 1 in airway smooth muscle: a potential pathway that modulates bronchial hyper-responsiveness in asthma?. Respir. Res. 1 (2000) 49-53
5. Barabasi A.L., and Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5 (2004) 101-113
6. Barnes P.J. New drugs for asthma. Nat. Rev. Drug. Discov. 3 (2004) 831-844
7. Barreiro O., Yanez-Mo M., Serrador J.M., Montoya M.C., Vicente-Manzanares M., Tejedor R., Furthmayr H., and Sanchez-Madrid F. Dynamic interaction of VCAM-1 and ICAM-1 with moesin and ezrin in a novel endothelial docking structure for adherent leukocytes. J. Cell Biol. 157 (2002) 1233-1245
8. Batagelj V., and Mrvar A. Pajek: program for large network analysis. Connections 21 (1998) 47-57
9. Bates M.E., Busse W.W., and Bertics P.J. Interleukin 5 signals through Shc and Grb2 in human eosinophils. Am. J. Respir. Cell Mol. Biol. 18 (1998) 75-83
10. Brandes U. A faster algorithm for betweenness centrality. J. Math. Sociol. 25 (2001) 163-177
11. Bruzzaniti A., Neff L., Sanjay A., Horne W.C., De Camilli P., and Baron R. Dynamin forms a src kinase-sensitive complex with Cbl and regulates podosomes and osteoclast activity. Mol. Biol. Cell 16 (2005) 3301-3313
12. Cardozo A.K., Berthou L., Kruhoffer M., Orntoft T., Nicolls M.R., and Eizirik D.L. Gene microarray study corroborates proteomic findings in rodent islet cells. J. Proteome Res. 2 (2003) 553-555
13. Darnell Jr. J.E., Kerr I.M., and Stark G.R. Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins. Science 264 (1994) 1415-1421
14. Diao Y., Li M., Feng Z., Yin J., and Pan Y. The community structure of human cellular signaling network. J. Theor. Biol. 247 (2007) 608-615
15. Draghici S., Khatri P., Martins R.P., Ostermeier G.C., and Krawetz S.A. Global functional profiling of gene expression. Genomics 81 (2003) 98-104
16. Edgar R., Domrachev M., and Lash A.E. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30 (2002) 207-210
17. Freeman L.C. A set of measures of centrality based on betweenness. Sociometry 40 (1977) 35-41
18. Freudenberg J., and Propping P. A similarity-based method for genome-wide prediction of disease-relevant human genes. Bioinformatics 18 Suppl. 2 (2002) S110-S115
19. Gavett S.H., O'Hearn D.J., Karp C.L., Patel E.A., Schofield B.H., Finkelman F.D., and Wills-Karp M. Interleukin-4 receptor blockade prevents airway responses induced by antigen challenge in mice. Am. J. Physiol. 272 (1997) L253-L261
20. Girvan M., and Newman M.E. Community structure in social and biological networks. Proc. Natl. Acad. Sci. 99 (2002) 7821-7826
21. Greenbaum D., Colangelo C., Williams K., and Gerstein M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol. 4 (2003) 117
22. Griffin T.J., Gygi S.P., Ideker T., Rist B., Eng J., Hood L., and Aebersold R. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell Proteomics 1 (2002) 323-333
23. Hamosh A., Scott A.F., Amberger J.S., Bocchini C.A., and McKusick V.A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33 (2005) D514-D517
24. Han J.D., Bertin N., Hao T., Goldberg D.S., Berriz G.F., Zhang L.V., Dupuy D., Walhout A.J., Cusick M.E., Roth F.P., and Vidal M. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430 (2004) 88-93
25. Harris M.A., Clark J., Ireland A., Lomax J., Ashburner M., Foulger R., Eilbeck K., Lewis S., Marshall B., Mungall C., Richter J., Rubin G.M., Blake J.A., Bult C., Dolan M., Drabkin H., Eppig J.T., Hill D.P., Ni L., Ringwald M., Balakrishnan R., Cherry J.M., Christie K.R., Costanzo M.C., Dwight S.S., Engel S., Fisk D.G., Hirschman J.E., Hong E.L., Nash R.S., Sethuraman A., Theesfeld C.L., Botstein D., Dolinski K., Feierbach B., Berardini T., Mundodi S., Rhee S.Y., Apweiler R., Barrell D., Camon E., Dimmer E., Lee V., Chisholm R., Gaudet P., Kibbe W., Kishore R., Schwarz E.M., Sternberg P., Gwinn M., Hannick L., Wortman J., Berriman M., Wood V., de la Cruz N., Tonellato P., Jaiswal P., Seigfried T., and White R. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32 (2004) D258-D261
26. Hewson C.A., Edbrooke M.R., and Johnston S.L. PMA induces the MUC5AC respiratory mucin in human bronchial epithelial cells, via PKC, EGF/TGF-alpha, Ras/Raf, MEK, ERK and Sp1-dependent mechanisms. J. Mol. Biol. 344 (2004) 683-695
27. Jeong H., Tombor B., Albert R., Oltvai Z.N., and Barabasi A.L. The large-scale organization of metabolic networks. Nature 407 (2000) 651-654
28. Jeong H., Mason S.P., Barabasi A.L., and Oltvai Z.N. Lethality and centrality in protein networks. Nature 411 (2001) 41-42
29. Jiang H., Harris M.B., and Rothman P. IL-4/IL-13 signaling beyond JAK/STAT. J. Allergy Clin. Immunol. 105 (2000) 1063-1070
30. Kabesch M., Schedel M., Carr D., Woitsch B., Fritzsch C., Weiland S.K., and von Mutius E. IL-4/IL-13 pathway genetics strongly influence serum IgE levels and childhood asthma. J. Allergy Clin. Immunol. 117 (2006) 269-274
31. Karoor V., Wang L., Wang H.Y., and Malbon C.C. Insulin stimulates sequestration of beta-adrenergic receptors and enhanced association of beta-adrenergic receptors with Grb2 via tyrosine 350. J. Biol. Chem. 273 (1998) 33035-33041
32. Kim D.H., Noh J.D., and Jeong H. Scale-free trees: the skeletons of complex networks. Phys. Rev. E Stat. Nonlinear Soft Matter Phys. 70 (2004) 046126
33. Kim P.J., and Jeong H. Reliability of rank order in sampled networks. Eur. Phys. J. B 55 (2007) 109-114
34. Kumar S., Pandey P., Bharti A., Jin S., Weichselbaum R., Weaver D., Kufe D., and Kharbanda S. Regulation of DNA-dependent protein kinase by the Lyn tyrosine kinase. J. Biol. Chem. 273 (1998) 25654-25658
35. Kurosaki T., Takata M., Yamanashi Y., Inazu T., Taniguchi T., Yamamoto T., and Yamamura H. Syk activation by the Src-family tyrosine kinase in the B cell receptor signaling. J. Exp. Med. 179 (1994) 1725-1729
36. Lee J.W., and Juliano R. Mitogenic signal transduction by integrin- and growth factor receptor-mediated pathways. Mol. Cells 17 (2004) 188-202
37. Lee S.H., Kim P.J., and Jeong H. Statistical properties of sampled networks. Phys. Rev. E Stat. Nonlinear Soft Matter Phys. 73 (2006) 016102
38. Levitt R.C., McLane M.P., MacDonald D., Ferrante V., Weiss C., Zhou T., Holroyd K.J., and Nicolaides N.C. IL-9 pathway in asthma: new therapeutic targets for allergic inflammatory disorders. J. Allergy Clin. Immunol. 103 (1999) S485-S491
39. Litonjua A., Thorn C.F., and Liggett S.B. Beta-Agonist and Beta-Blocker Pathway (2005), PharmGKB
40. Luttrell L.M., Ferguson S.S., Daaka Y., Miller W.E., Maudsley S., Della Rocca G.J., Lin F., Kawakatsu H., Owada K., Luttrell D.K., Caron M.G., and Lefkowitz R.J. Beta-arrestin-dependent formation of beta2 adrenergic receptor-Src protein kinase complexes. Science 283 (1999) 655-661
41. MacPartlin M., Zeng S., Lee H., Stauffer D., Jin Y., Thayer M., and Lu H. p300 regulates p63 transcriptional activity. J. Biol. Chem. 280 (2005) 30604-30610
42. Malerba G., and Pignatti P.F. A review of asthma genetics: gene expression studies and recent candidates. J. Appl. Genet. 46 (2005) 93-104
43. Martinon F., Holler N., Richard C., and Tschopp J. Activation of a pro-apoptotic amplification loop through inhibition of NF-kappaB-dependent survival signals by caspase-mediated inactivation of RIP. FEBS Lett. 468 (2000) 134-136
44. Mijalski T., Harder A., Halder T., Kersten M., Horsch M., Strom T.M., Liebscher H.V., Lottspeich F., de Angelis M.H., and Beckers J. Identification of coexpressed gene clusters in a comparative analysis of transcriptome and proteome in mouse tissues. Proc. Natl. Acad. Sci. 102 (2005) 8621-8626
45. Mitra S.K., Hanson D.A., and Schlaepfer D.D. Focal adhesion kinase: in command and control of cell motility. Nat. Rev. Mol. Cell Biol. 6 (2005) 56-68
46. Moore D.S. Goodness-of-Fit Techniques (1986), Marcel Dekker, New York
47. Mullen A.C., High F.A., Hutchins A.S., Lee H.W., Villarino A.V., Livingston D.M., Kung A.L., Cereb N., Yao T.P., Yang S.Y., and Reiner S.L. Role of T-bet in commitment of TH1 cells before IL-12-dependent selection. Science 292 (2001) 1907-1910
48. Nakashima K., Hirota T., Obara K., Shimizu M., Jodo A., Kameda M., Doi S., Fujita K., Shirakawa T., Enomoto T., Kishi F., Yoshihara S., Matsumoto K., Saito H., Suzuki Y., Nakamura Y., and Tamari M. An association study of asthma and related phenotypes with polymorphisms in negative regulator molecules of the TLR signaling pathway. J. Hum. Genet. 51 (2006) 284-291
49. Ogata H., Goto S., Sato K., Fujibuchi W., Bono H., and Kanehisa M. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 27 (1999) 29-34
50. Okkenhaug K., and Rottapel R. Grb2 forms an inducible protein complex with CD28 through a Src homology 3 domain-proline interaction. J. Biol. Chem. 273 (1998) 21194-21202
51. Pastor-Satorras R., Smith E., and Sole R.V. Evolving protein interaction networks through gene duplication. J. Theor. Biol. 222 (2003) 199-210
52. Payne D.N., Rogers A.V., Adelroth E., Bandi V., Guntupalli K.K., Bush A., and Jeffery P.K. Early thickening of the reticular basement membrane in children with difficult asthma. Am. J. Respir. Crit. Care Med. 167 (2003) 78-82
53. Perez-Iratxeta C., Bork P., and Andrade M.A. Association of genes to genetically inherited diseases using data mining. Nat. Genet. 31 (2002) 316-319
54. Peri S., Navarro J.D., Kristiansen T.Z., Amanchy R., Surendranath V., Muthusamy B., Gandhi T.K., Chandrika K.N., Deshpande N., Suresh S., Rashmi B.P., Shanker K., Padma N., Niranjan V., Harsha H.C., Talreja N., Vrushabendra B.M., Ramya M.A., Yatish A.J., Joy M., Shivashankar H.N., Kavitha M.P., Menezes M., Choudhury D.R., Ghosh N., Saravana R., Chandran S., Mohan S., Jonnalagadda C.K., Prasad C.K., Kumar-Sinha C., Deshpande K.S., and Pandey A. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res. 32 (2004) D497-D501
55. Pernis A.B., and Rothman P.B. JAK-STAT signaling in asthma. J. Clin. Invest. 109 (2002) 1279-1283
56. Sabidussi G. The centrality index of a graph. Psychometrika 31 (1966) 581-603
57. Son S.W., and Jeong H. Reconstruction of a genetic network from gene perturbation data. J. Kor. Phys. Soc. 48 (2006) S208
58. Son S.W., Kim D.H., Ahn Y.Y., and Jeong H. Response network emerging from simple perturbation. J. Kor. Phys. Soc. 44 (2004) 628-632
59. Stelzl U., Worm U., Lalowski M., Haenig C., Brembeck F.H., Goehler H., Stroedicke M., Zenkner M., Schoenherr A., Koeppen S., Timm J., Mintzlaff S., Abraham C., Bock N., Kietzmann S., Goedde A., Toksoz E., Droege A., Krobitsch S., Korn B., Birchmeier W., Lehrach H., and Wanker E.E. A human protein-protein interaction network: a resource for annotating the proteome. Cell 122 (2005) 957-968
60. Tattersfield A.E., Knox A.J., Britton J.R., and Hall I.P. Asthma. Lancet 360 (2002) 1313-1322
61. Tavazoie S., Hughes J.D., Campbell M.J., Cho R.J., and Church G.M. Systematic determination of genetic network architecture. Nat. Genet. 22 (1999) 281-285
62. Thode Jr. H.C. Testing for Normality (2002), Marcel Dekker, New York
63. Tiffin N., Kelso J.F., Powell A.R., Pan H., Bajic V.B., and Hide W.A. Integration of text- and datamining using ontologies successfully selects disease gene candidates. Nucleic Acids Res. 33 (2005) 1544-1552
64. Troyanskaya O.G., Garber M.E., Brown P.O., Botstein D., and Altman R.B. Nonparametric methods for identifying differentially expressed genes in microarray data. Bioinformatics 18 (2002) 1454-1461
65. Turki J., Pak J., Green S.A., Martin R.J., and Liggett S.B. Genetic polymorphisms of the beta 2-adrenergic receptor in nocturnal and nonnocturnal asthma. Evidence that Gly16 correlates with the nocturnal phenotype. J. Clin. Invest. 95 (1995) 1635-1641
66. Usacheva A., Tian X., Sandoval R., Salvi D., Levy D., and Colamonici O.R. The WD motif-containing protein RACK-1 functions as a scaffold protein within the type I IFN receptor-signaling complex. J. Immunol. 171 (2003) 2989-2994
67. Vignola A.M., Chiappara G., Siena L., Bruno A., Gagliardo R., Merendino A.M., Polla B.S., Arrigo A.P., Bonsignore G., Bousquet J., and Chanez P. Proliferation and activation of bronchial epithelial cells in corticosteroid-dependent asthma. J. Allergy Clin. Immunol. 108 (2001) 738-746
68. Walpole R.E., and Myers R.H. Probability and Statistics for Engineers and Scientists (1993), Macmillan, New York
69. Wills-Karp M., Luyimbazi J., Xu X., Schofield B., Neben T.Y., Karp C.L., and Donaldson D.D. Interleukin-13: central mediator of allergic asthma. Science 282 (1998) 2258-2261
70. Yarwood S.J., Steele M.R., Scotland G., Houslay M.D., and Bolger G.B. The RACK1 signaling scaffold protein selectively interacts with the cAMP-specific phosphodiesterase PDE4D5 isoform. J. Biol. Chem. 274 (1999) 14909-14917