Shift in chicken intestinal gene association networks after infection with Salmonella

Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics

Volumn 6, Issue 4, 2011, Pages 339-347

  Schokker, Dirkjan ^a   De Koning, Dirk Jan ^b   Rebel, Johanna M J ^a   Smits, Mari A ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

Chicken; Gene Associated Network; Gene expression; Hubs; Jejunum; Salmonella enteritidis

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CHICKEN; CONTROLLED STUDY; GENE EXPRESSION; GENE IDENTIFICATION; INTESTINE INFECTION; MALE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; SALMONELLA ENTERITIDIS; SALMONELLOSIS;

ANIMALIA; GALLUS GALLUS; SALMONELLA; SALMONELLA ENTERITIDIS;

EID: 80755140691     PISSN: 1744117X     EISSN: 18780407     Source Type: Journal    
DOI: 10.1016/j.cbd.2011.07.004     Document Type: Article

References (76)

1. R. Albert Scale-free networks in cell biology J. Cell Sci. 118 2005 4947 4957 (Pubitemid 41672427)
2. I. Amit, M. Garber, N. Chevrier, A.P. Leite, Y. Donner, T. Eisenhaure, M. Guttman, J.K. Grenier, W.B. Li, O. Zuk, L.A. Schubert, B. Birditt, T. Shay, A. Goren, X.L. Zhang, Z. Smith, R. Deering, R.C. McDonald, M. Cabili, B.E. Bernstein, J.L. Rinn, A. Meissner, D.E. Root, N. Hacohen, and A. Regev Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses Science 326 2009 257 263
3. A.L. Barabasi, and R. Albert Emergence of scaling in random networks Science 286 1999 509 512
4. A.L. Barabasi, and Z.N. Oltvai Network biology: understanding the cell's functional organization Nat. Rev. Genet. 5 2004 101 113 (Pubitemid 38160277)
5. P.A. Barrow, M.B. Huggins, M.A. Lovell, and J.M. Simpson Observations on the pathogenesis of experimental Salmonella typhimurium infection in chickens Res. Vet. Sci. 42 1987 194 199
6. F. Basmaji, H. Martin-Yken, F. Durand, A. Dagkessamanskaia, C. Pichereaux, M. Rossignol, and J. Francois The 'interactome' of the Knr4/Smi1, a protein implicated in coordinating cell wall synthesis with bud emergence in Saccharomyces cerevisiae Mol. Genet. Genomics 275 2006 217 230 (Pubitemid 43361887)
7. L. Chappell, P. Kaiser, P. Barrow, M.A. Jones, C. Johnston, and P. Wigley The immunobiology of avian systemic salmonellosis Vet. Immunol. Immunopathol. 128 2009 53 59
8. J.H. Cheeseman, M.G. Kaiser, C. Ciraci, P. Kaiser, and S.J. Lamont Breed effect on early cytokine mRNA expression in spleen and cecum of chickens with and without Salmonella enteritidis infection Dev. Comp. Immunol. 31 2007 52 60 (Pubitemid 44436562)
9. H.I. Chiang, C.L. Swaggerty, M.H. Kogut, S.E. Dowd, X. Li, I.Y. Pevzner, and H. Zhou Gene expression profiling in chicken heterophils with Salmonella enteritidis stimulation using a chicken 44 K Agilent microarray BMC Genomics 9 2008 526
10. S.E. Crawford, V. Stellmach, J.E. Murphy-Ullrich, S.M.F. Ribeiro, J. Lawler, R.O. Hynes, G.P. Boivin, and N. Bouck Thrombospondin-1 is a major activator of TGF-beta 1 in vivo Cell 93 1998 1159 1170 (Pubitemid 28307421)
11. L.D. D'Andrea, and L. Regan TPR proteins: the versatile helix Trends Biochem. Sci. 28 2003 655 662 (Pubitemid 37500900)
12. G. Dennis, B.T. Sherman, D.A. Hosack, J. Yang, W. Gao, H.C. Lane, and R.A. Lempicki DAVID: Database for annotation, visualization, and integrated discovery Genome Biol. 4 2003
13. A. Fridkin, A. Penkner, V. Jantsch, and Y. Gruenbaum SUN-domain and KASH-domain proteins during development, meiosis and disease Cell. Mol. Life Sci. 66 2009 1518 1533
14. J. Friedman, T. Hastie, and R. Tibshirani Sparse inverse covariance estimation with the graphical lasso Biostatistics 9 2008 432 441 (Pubitemid 351882084)
15. W.J. Gehring, M. Affolter, and T. Burglin Homeodomain proteins Annu. Rev. Biochem. 63 1994 487 526 (Pubitemid 24218641)
16. U. Gether, and B.K. Kobilka G protein-coupled receptors - II. Mechanism of agonist activation J. Biol. Chem. 273 1998 17979 17982
17. A. Geyra, Z. Uni, and D. Sklan Enterocyte dynamics and mucosal development in the posthatch chick Poult. Sci. 80 2001 776 782 (Pubitemid 33659848)
18. G. Giaever, A.M. Chu, L. Ni, C. Connelly, L. Riles, S. Veronneau, S. Dow, A. Lucau-Danila, K. Anderson, B. Andre, A.P. Arkin, A. Astromoff, M. El-Bakkoury, R. Bangham, R. Benito, S. Brachat, S. Campanaro, M. Curtiss, K. Davis, A. Deutschbauer, K.D. Entian, P. Flaherty, F. Foury, D.J. Garfinkel, M. Gerstein, D. Gotte, U. Guldener, J.H. Hegemann, S. Hempel, Z. Herman, D.F. Jaramillo, D.E. Kelly, S.L. Kelly, P. Kotter, D. LaBonte, D.C. Lamb, N. Lan, H. Liang, H. Liao, L. Liu, C. Luo, M. Lussier, R. Mao, P. Menard, S.L. Ooi, J.L. Revuelta, C.J. Roberts, M. Rose, P. Ross-Macdonald, B. Scherens, G. Schimmack, B. Shafer, D.D. Shoemaker, S. Sookhai-Mahadeo, R.K. Storms, J.N. Strathern, G. Valle, M. Voet, G. Volckaert, C.Y. Wang, T.R. Ward, J. Wilhelmy, E.A. Winzeler, Y. Yang, G. Yen, E. Youngman, K. Yu, H. Bussey, J.D. Boeke, M. Snyder, P. Philippsen, R.W. Davis, and M. Johnston Functional profiling of the Saccharomyces cerevisiae genome Nature 418 2002 387 391 (Pubitemid 34826834)
19. W. Gish, and D.J. States Identification of protein coding regions by database similarity search Nat. Genet. 3 1993 266 272 (Pubitemid 23096565)
20. L.S. Goldstein With apologies to scheherazade: tails of 1001 kinesin motors Annu. Rev. Genet. 27 1993 319 351 (Pubitemid 24011357)
21. A. Guilherme, N.A. Soriano, S. Bose, J. Holik, A. Bose, D.P. Pomerleau, P. Furcinitti, J. Leszyk, S. Corvera, and M.P. Czech EHD2 and the novel EH domain binding protein EHBP1 couple endocytosis to the actin cytoskeleton J. Biol. Chem. 279 2004 10593 10605 (Pubitemid 38372671)
22. B.Z. Harris, and W.A. Lim Mechanism and role of PDZ domains in signaling complex assembly J. Cell Sci. 114 2001 3219 3231 (Pubitemid 32998900)
23. H.N. Higgs Formin proteins: a domain-based approach Trends Biochem. Sci. 30 2005 342 353 (Pubitemid 40799053)
24. D.W. Huang, B.T. Sherman, Q. Tan, J.R. Collins, W.G. Alvord, J. Roayaei, R. Stephens, M.W. Baseler, H.C. Lane, and R.A. Lempicki The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists Genome Biol. 8 9 2007 R183
25. A. Ilias, Z. Urban, T.L. Seidl, O. Le Saux, E. Sinko, C.D. Boyd, B. Sarkadi, and A. Varadi Loss of ATP-dependent transport activity in pseudoxanthoma elasticum-associated mutants of human ABCC6 (MRP6) J. Biol. Chem. 277 2002 16860 16867 (Pubitemid 34967710)
26. E.B. Ives, J. Nichols, S.R. Wente, and J.D. York Biochemical and functional characterization of inositol 1,3,4,5,6-pentakisphosphate 2-kinases J. Biol. Chem. 275 2000 36575 36583 (Pubitemid 32002056)
27. T.H. Ji, M. Grossmann, and I.H. Ji G protein-coupled receptors I. Diversity of receptor-ligand interactions J. Biol. Chem. 273 1998 17299 17302 (Pubitemid 28355051)
28. M. Johnson, I. Zaretskaya, Y. Raytselis, Y. Merezhuk, S. McGinnis, and T.L. Madden NCBI BLAST: a better web interface Nucleic Acids Res. 36 2008 W5 W9
29. M.G. Kaiser, J.H. Cheesernan, P. Kaiser, and S.J. Lamont Cytokine expression in chicken peripheral blood mononuclear cells after in vitro exposure to Salmonella enterica serovar enteritidis Poult. Sci. 85 2006 1907 1911 (Pubitemid 44583322)
30. J.G. Kiang, and G.C. Tsokos Heat shock protein 70 kDa: molecular biology, biochemistry, and physiology Pharmacol. Ther. 80 1998 183 201 (Pubitemid 28498227)
31. S.Y. Kim, S. Imoto, and S. Miyano Inferring gene networks from time series microarray data using dynamic Bayesian networks Brief Bioinform. 4 2003 228 235
32. M.H. Kogut, G.I. Tellez, E.D. McGruder, B.M. Hargis, J.D. Williams, D.E. Corrier, and J.R. DeLoach Heterophils are decisive components in the early responses of chickens to Salmonella enteritidis infections Microb. Pathog. 16 1994 141 151 (Pubitemid 24176406)
33. J.E. Kwon, M. La, K.H. Oh, Y.M. Oh, G.R. Kim, J.H. Seol, S.H. Baek, T. Chiba, K. Tanaka, O.S. Bang, C.O. Joe, and C.H. Chung BTB domain-containing speckle-type POZ protein (SPOP) serves as an adaptor of Daxx for ubiquitination by Cul3-based ubiquitin ligase J. Biol. Chem. 281 2006 12664 12672 (Pubitemid 43855356)
34. M. Lebel, P. Agarwal, C.W. Cheng, M.G. Kabir, T.Y. Chan, V. Thanabalasingham, X. Zhang, D.R. Cohen, M. Husain, S.H. Cheng, B.G. Bruneau, and C.C. Hui The Iroquois homeobox gene Irx2 is not essential for normal development of the heart and midbrain-hindbrain boundary in mice Mol. Cell. Biol. 23 2003 8216 8225 (Pubitemid 37377511)
35. R.J. Lefkowitz G protein-coupled receptors III. New roles for receptor kinases and beta-arrestins in receptor signaling and desensitization J. Biol. Chem. 273 1998 18677 18680 (Pubitemid 28366245)
36. C.Y. Lin, C.H. Chin, H.H. Wu, S.H. Chen, C.W. Ho, and M.T. Ko Hubba: hub objects analyzer - a framework of interactome hubs identification for network biology Nucleic Acids Res. 36 2008 W438 W443
37. A. Marchler-Bauer, and S.H. Bryant CD-Search: protein domain annotations on the fly Nucleic Acids Res. 32 2004 W327 W331
38. A. Marchler-Bauer, J.B. Anderson, P.F. Cherukuri, C. DeWeese-Scott, L.Y. Geer, M. Gwadz, S. He, D.I. Hurwitz, J.D. Jackson, Z. Ke, C.J. Lanczycki, C.A. Liebert, C. Liu, F. Lu, G.H. Marchler, M. Mullokandov, B.A. Shoemaker, V. Simonyan, J.S. Song, P.A. Thiessen, R.A. Yamashita, J.J. Yin, D. Zhang, and S.H. Bryant CDD: a Conserved Domain Database for protein classification Nucleic Acids Res. 33 2005 D192 D196
39. C. Maris, C. Dominguez, and F.H.T. Allain The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression FEBS J. 272 2005 2118 2131 (Pubitemid 40655326)
40. P.E. Meyer, F. Lafitte, and G. Bontempi minet: A R/Bioconductor package for inferring large transcriptional networks using mutual information BMC Bioinforma. 9 2008 461
41. A. Morgulis, G. Coulouris, Y. Raytselis, T.L. Madden, R. Agarwala, and A.A. Schaffer Database indexing for production MegaBLAST searches Bioinformatics 24 2008 1757 1764
42. T. Nishi, and M. Forgac The vacuolar (H+)-ATPases-nature's most versatile proton pumps Nat. Rev. Mol. Cell Biol. 3 2002 94 103
43. R. Opgen-Rhein, and K. Strimmer From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data BMC Syst. Biol. 1 2007 37
44. R. Opgen-Rhein, and K. Strimmer Learning causal networks from systems biology time course data: an effective model selection procedure for the vector autoregressive process BMC Bioinforma. 8 Suppl. 2 2007 S3
45. F. Palmieri The mitochondrial transporter family (SLC25): physiological and pathological implications Pflugers Arch. Eur. J. Physiol. 447 2004 689 709 (Pubitemid 38241455)
46. V.E. Papaioannou, and L.M. Silver The T-box gene family Bioessays 20 1998 9 19 (Pubitemid 28111327)
47. O. Polgar, and S.E. Bates ABC transporters in the balance: is there a role in multidrug resistance? Biochem. Soc. Trans. 33 2005 241 245 (Pubitemid 40313812)
48. N. Przulj, D.A. Wigle, and I. Jurisica Functional topology in a network of protein interactions Bioinformatics 20 2004 340 348 (Pubitemid 38262765)
49. M. Rebhan, V. ChalifaCaspi, J. Prilusky, and D. Lancet GeneCards: Integrating information about genes, proteins and diseases Trends Genet. 13 1997 163 (Pubitemid 127739947)
50. J. Rung, T. Schlitt, A. Brazma, K. Freivalds, and J. Vilo Building and analysing genome-wide gene disruption networks Bioinformatics 18 Suppl. 2 2002 S202 S210
51. K. Saito, J. Murai, H. Kajiho, K. Kontani, H. Kurosu, and T. Katada A novel binding protein composed of homophilic tetramer exhibits unique properties for the small GTPase Rab5 J. Biol. Chem. 277 2002 3412 3418 (Pubitemid 34953210)
52. G. Scardoni, M. Petterlini, and C. Laudanna Analyzing biological network parameters with CentiScaPe Bioinformatics 25 2009 2857 2859
53. J. Schafer, and K. Strimmer An empirical Bayes approach to inferring large-scale gene association networks Bioinformatics 21 2005 754 764 (Pubitemid 40439411)
54. J. Schafer, and K. Strimmer A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics Stat. Appl. Genet. Mol. Biol. 4 2005 (Article 32)
55. J.R. Schoenborn, and C.B. Wilson Regulation of interferon-gamma during innate and adaptive immune responses Adv. Immunol. 96 96 2007 41 101 (Pubitemid 350018717)
56. D. Schokker, A.J. Hoekman, M.A. Smits, and J.M. Rebel Gene expression patterns associated with chicken jejunal development Dev. Comp. Immunol. 33 2009 1156 1164
57. D. Schokker, M.A. Smits, A.J. Hoekman, H.K. Parmentier, and J.M. Rebel Effects of Salmonella on spatial-temporal processes of jejunal development in chickens Dev. Comp. Immunol. 34 2010 1090 1100
58. P. Shannon, A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker Cytoscape: a software environment for integrated models of biomolecular interaction networks Genome Res. 13 2003 2498 2504 (Pubitemid 37428274)
59. R.G. Shaw, and T. Mitchellolds Anova for Unbalanced Data - an Overview Ecology 74 1993 1638 1645
60. F.M. Speed, R.R. Hocking, and O.P. Hackney Methods of analysis of linear-models with unbalanced data J. Am. Stat. Assoc. 73 1978 105 112
61. J.E. Stajich, D. Block, K. Boulez, S.E. Brenner, S.A. Chervitz, C. Dagdigian, G. Fuellen, J.G.R. Gilbert, I. Korf, H. Lapp, H. Lehvaslaiho, C. Matsalla, C.J. Mungall, B.I. Osborne, M.R. Pocock, P. Schattner, M. Senger, L.D. Stein, E. Stupka, M.D. Wilkinson, and E. Birney The bioperl toolkit: Perl modules for the life sciences Genome Res. 12 2002 1611 1618 (Pubitemid 35175100)
62. S. Suzuki Pathogenicity of Salmonella enteritidis in poultry Int. J. Food Microbiol. 21 1994 89 105 (Pubitemid 24074904)
63. R. Thomas, D. Thieffry, and M. Kaufman Dynamical behaviour of biological regulatory networks-I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state Bull. Math. Biol. 57 1995 247 276
64. W. Tian, L.V. Zhang, M. Tasan, F.D. Gibbons, O.D. King, J. Park, Z. Wunderlich, J.M. Cherry, and F.P. Roth Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function Genome Biol. 9 Suppl. 1 2008 S7
65. S. van Hemert, A.J.W. Hoekman, M.A. Smits, and J.M.J. Rebel Early host gene expression responses to a Salmonella infection in the intestine of chickens with different genetic background examined with cDNA and oligonucleotide microarrays Comp. Biochem. Physiol. D 2006 292 299 (Pubitemid 44437814)
66. S. van Hemert, A.J.W. Hoekman, M.A. Smits, and J.M.J. Rebel Gene expression responses to a Salmonella infection in the chicken intestine differ between lines Vet. Immunol. Immunopathol. 114 2006 247 258 (Pubitemid 44634730)
67. S. Van Hemert, A.J.W. Hoekman, M.A. Smits, and J.M.J. Rebel Immunological and gene expression responses to a Salmonella infection in the chicken intestine Vet. Res. 38 2007 51 63
68. F.G. van Zijderveld, A.M. van Zijderveld-van Bemmel, and J. Anakotta Comparison of four different enzyme-linked immunosorbent assays for serological diagnosis of Salmonella enteritidis infections in experimentally infected chickens J. Clin. Microbiol. 30 1992 2560 2566
69. I. Voigt, S.A. Camacho, B.A. de Boer, M. Lipp, R. Forster, and C. Berek CXCR5-deficient mice develop functional germinal centers in the splenic T cell zone Eur. J. Immunol. 30 2000 560 567 (Pubitemid 30098849)
70. X. Wang, D.M. Truckses, S. Takada, T. Matsumura, N. Tanese, and R.H. Jacobson Conserved region I of human coactivator TAF4 binds to a short hydrophobic motif present in transcriptional regulators Proc. Natl. Acad. Sci. U. S. A. 104 2007 7839 7844 (Pubitemid 47185838)
71. Y. Wei, S. Liu, J. Lausen, C. Woodrell, S. Cho, N. Biris, N. Kobayashi, S. Yokoyama, and M.H. Werner A TAF4-homology domain from the corepressor ETO is a docking platform for positive and negative regulators of transcription Nat. Struct. Mol. Biol. 14 2007 653 661 (Pubitemid 47037065)
72. G.S. Withanage, P. Kaiser, P. Wigley, C. Powers, P. Mastroeni, H. Brooks, P. Barrow, A. Smith, D. Maskell, and I. McConnell Rapid expression of chemokines and proinflammatory cytokines in newly hatched chickens infected with Salmonella enterica serovar typhimurium Infect. Immun. 72 2004 2152 2159 (Pubitemid 38419929)
73. G.S.K. Withanage, P. Wigley, P. Kaiser, P. Mastroeni, H. Brooks, C. Powers, R. Beal, P. Barrow, D. Maskell, and I. McConnell Cytokine and chemokine responses associated with clearance of a primary Salmonella enterica serovar Typhimurium infection in the chicken and in protective immunity to rechallenge Infect. Immun. 73 2005 5173 5182 (Pubitemid 41105677)
74. X. Yu, C.C. Chini, M. He, G. Mer, and J. Chen The BRCT domain is a phospho-protein binding domain Science 302 2003 639 642 (Pubitemid 37310919)
75. S. Zhang, H.S. Lillehoj, C.H. Kim, C.L. Keeler Jr., U. Babu, and M.Z. Zhang Transcriptional response of chicken macrophages to Salmonella enterica serovar enteritidis infection Dev. Biol. (Basel) 132 2008 141 151
76. H. Zhou, and S.J. Lamont Global gene expression profile after Salmonella enterica Serovar enteritidis challenge in two F8 advanced intercross chicken lines Cytogenet Genome Res. 117 2007 131 138 (Pubitemid 47202673)