M. Hofstad, B. John, B. Calnek, W. Reid, H. Yoder et al., Diseases of Poultry, pp.65-123, 1992.

L. Kabir, Avian Colibacillosis and Salmonellosis: A Closer Look at Epidemiology, Pathogenesis, Diagnosis, Control and Public Health Concerns, International Journal of Environmental Research and Public Health, vol.7, issue.1, pp.89-114, 2010.
DOI : 10.3390/ijerph7010089

A. Wales and R. Davies, Typhimurium infection in laying hens, Avian Pathology, vol.64, issue.5, pp.429-436, 2011.
DOI : 10.2307/1588161

URL : https://hal.archives-ouvertes.fr/hal-00726663

L. Chappell, P. Kaiser, P. Barrow, M. Jones, C. Johnston et al., The immunobiology of avian systemic salmonellosis, Veterinary Immunology and Immunopathology, vol.128, issue.1-3, pp.53-59, 2009.
DOI : 10.1016/j.vetimm.2008.10.295

J. Guard-petter, The chicken, the egg and Salmonella enteritidis, Environmental Microbiology, vol.130, issue.7, pp.421-430, 2001.
DOI : 10.1016/S1369-5274(00)00187-9

M. Parker, Enteric infections.InTopley and Wilson's principles of bacteriology, virology and immunity, pp.424-446, 1990.

P. Barrow, M. Huggins, and M. Lovell, Host Specificity of Salmonella Infection in Chickens and Mice Is Expressed In Vivo Primarily at the Level of the Reticuloendothelial System, Infect Immun, vol.62, pp.4602-4610, 1994.

N. Bumstead and P. Barrow, Resistance to Salmonella gallinarum, S. pullorum, and S. enteritidis in Inbred Lines of Chickens, Avian Diseases, vol.37, issue.1, pp.189-193, 1993.
DOI : 10.2307/1591473

S. Van-hemert, A. Hoekman, M. Smits, and J. Rebel, Gene expression responses to a Salmonella infection in the chicken intestine differ between lines, Veterinary Immunology and Immunopathology, vol.114, issue.3-4, pp.247-258, 2006.
DOI : 10.1016/j.vetimm.2006.08.007

F. Calenge, P. Kaiser, A. Vignal, and C. Beaumont, Genetic control of resistance to salmonellosis and to Salmonella carrier-state in fowl: a review, Genetics Selection Evolution, vol.42, issue.1, pp.11-21, 2010.
DOI : 10.1186/1297-9686-42-11

S. Redmond, P. Chuammitri, C. Andreasen, D. Pali?, and S. Lamont, Proportion of circulating chicken heterophils and CXCLi2 expression in response to Salmonella enteritidis are affected by genetic line and immune modulating diet, Veterinary Immunology and Immunopathology, vol.140, issue.3-4, pp.323-328, 2011.
DOI : 10.1016/j.vetimm.2011.01.006

J. Hu, N. Bumstead, P. Barrow, G. Sebastiani, L. Olien et al., Resistance to Salmonellosis in the Chicken Is Linked to NRAMP1 and TNC, Genome Res, vol.7, pp.693-704, 1997.

G. Leveque, V. Forgetta, S. Morroll, A. Smith, N. Bumstead et al., Allelic Variation in TLR4 Is Linked to Susceptibility to Salmonella enterica Serovar Typhimurium Infection in Chickens, Infection and Immunity, vol.71, issue.3, pp.1116-1124, 2003.
DOI : 10.1128/IAI.71.3.1116-1124.2003

J. Sadeyen, J. Trotereau, P. Velge, J. Marly, C. Beaumont et al., Salmonella carrier state in chicken: comparison of expression of immune response genes between susceptible and resistant animals, Microbes and Infection, vol.6, issue.14, pp.1278-1286, 2004.
DOI : 10.1016/j.micinf.2004.07.005

M. Fife, N. Salmon, P. Hocking, and P. Kaiser, ), Animal Genetics, vol.125, issue.Suppl 1, pp.871-877, 2009.
DOI : 10.1111/j.1365-2052.2009.01930.x

Z. Pan, Q. Fang, S. Geng, X. Kang, Q. Cong et al., Analysis of immune-related gene expression in chicken peripheral blood mononuclear cells following Salmonella enterica serovar Enteritidis infection in vitro, Research in Veterinary Science, vol.93, issue.2, 2012.
DOI : 10.1016/j.rvsc.2011.12.018

D. Coble, S. Redmond, B. Hale, and S. Lamont, Distinct lines of chickens express different splenic cytokine profiles in response to Salmonella Enteritidis challenge, Poultry Science, vol.90, issue.8, pp.1659-1663, 2011.
DOI : 10.3382/ps.2010-01279

J. Galan and P. Cossart, Host???pathogen interactions: a diversity of themes, a variety of molecular machines, Current Opinion in Microbiology, vol.8, issue.1, pp.1-3, 2005.
DOI : 10.1016/j.mib.2004.12.015

S. Mattoo, Y. Lee, and J. Dixon, Interactions of bacterial effector proteins with host proteins, Current Opinion in Immunology, vol.19, issue.4, pp.392-401, 2007.
DOI : 10.1016/j.coi.2007.06.005

T. Pas, M. Van-hemert, S. Hulsegge, I. Rebel, J. Smits et al., A pathways analysis tool for analyzing microarray data of species with low physiological information, Adv Bioinf, 2008.

S. Van-hemert, A. Hoekman, M. Smits, and 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, Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, vol.1, issue.3, pp.292-299, 2006.
DOI : 10.1016/j.cbd.2006.05.001

D. Schokker, A. Hoekman, M. Smits, and J. Rebel, Gene expression patterns associated with chicken jejunal development, Developmental & Comparative Immunology, vol.33, issue.11, pp.1156-1164, 2009.
DOI : 10.1016/j.dci.2009.06.002

M. Crhanova, H. Hradecka, M. Faldynova, M. Matulova, H. Havlickova et al., Immune Response of Chicken Gut to Natural Colonization by Gut Microflora and to Salmonella enterica Serovar Enteritidis Infection, Infection and Immunity, vol.79, issue.7, pp.2755-2763, 2011.
DOI : 10.1128/IAI.01375-10

G. Marot, J. Foulley, and C. Mayer, Moderated effect size and P-value combinations for microarray meta-analyses, Bioinformatics, vol.25, issue.20, pp.2692-2699, 2009.
DOI : 10.1093/bioinformatics/btp444

URL : https://hal.archives-ouvertes.fr/hal-00782348

L. Hedges and I. Olkin, Statistical Methods for Meta-Analysis, 1985.

D. Stangl and D. Berry, Meta-Analysis in Medicine and Health Policy, 2000.
DOI : 10.1201/9780203909935

D. Schokker, M. Smits, A. Hoekman, H. Parmentier, and J. Rebel, Effects of Salmonella on spatial-temporal processes of jejunal development in chickens, Developmental & Comparative Immunology, vol.34, issue.10, pp.1090-1100, 2010.
DOI : 10.1016/j.dci.2010.05.013

M. Fife, J. Howel, N. Salmon, P. Hocking, P. Van-diemen et al., Genome-wide SNP analysis identifies major QTL for Salmonella colonization in the chicken, Animal Genetics, vol.55, issue.Suppl. 1, pp.134-140, 2010.
DOI : 10.1111/j.1365-2052.2010.02090.x

P. Barrow, N. Bumstead, K. Marston, M. Lovell, and P. Wigley, Faecal shedding and intestinal colonization of Salmonella enterica in in-bred chickens: the effect of host-genetic background, Epidemiology and Infection, vol.132, issue.1, pp.117-126, 2003.
DOI : 10.1017/S0950268803001274

D. Schokker, T. Peters, A. Hoekman, J. Rebel, and M. Smits, Differences in the early response of hatchlings of different chicken breeding lines to Salmonella enterica serovar Enteritidis infection, Poultry Science, vol.91, issue.2, 2012.
DOI : 10.3382/ps.2011-01758

G. Smyth, Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments, Statistical Applications in Genetics and Molecular Biology, vol.3, issue.1, 2004.
DOI : 10.2202/1544-6115.1027

M. Ritchie, J. Silver, A. Oshlack, M. Holmes, D. Diyagama et al., A comparison of background correction methods for two-colour microarrays, Bioinformatics, vol.23, issue.20, pp.2700-2707, 2007.
DOI : 10.1093/bioinformatics/btm412

D. Huang, B. Sherman, and R. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nature Protocols, vol.99, issue.1, pp.44-57, 2009.
DOI : 10.1038/nprot.2008.211

D. Huang, B. Sherman, and R. Lempicki, Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists, Nucleic Acids Research, vol.37, issue.1, pp.1-13, 2009.
DOI : 10.1093/nar/gkn923

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: A practical and powerful approach to multiple testing, J R Stat Soc B, vol.57, pp.289-300, 1995.

A. Befus, N. Johnston, G. Leslie, and J. Bienenstock, Gut-associated lymphoid tissue in the chicken. I. Morphology, ontogeny, and some functional characteristics of Peyer's patches, J Immunol, vol.125, pp.2626-2632, 1980.

D. Barford, A. Das, and M. Egloff, THE STRUCTURE AND MECHANISM OF PROTEIN PHOSPHATASES: Insights into Catalysis and Regulation, Annual Review of Biophysics and Biomolecular Structure, vol.27, issue.1, pp.133-164, 1998.
DOI : 10.1146/annurev.biophys.27.1.133

P. Van-weeren, K. De-bruyn, A. De-vries-smits, J. Van-lint, and B. Burgering, Essential Role for Protein Kinase B (PKB) in Insulin-induced Glycogen Synthase Kinase 3 Inactivation: CHARACTERIZATION OF DOMINANT-NEGATIVE MUTANT OF PKB, Journal of Biological Chemistry, vol.273, issue.21, pp.13150-13156, 1998.
DOI : 10.1074/jbc.273.21.13150

N. Blom, T. Sicheritz-pontén, R. Gupta, S. Gammeltoft, and S. Brunak, Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence, PROTEOMICS, vol.4, issue.6, pp.1633-1649, 2004.
DOI : 10.1002/pmic.200300771

J. Daniel and A. Reynolds, Tyrosine phosphorylation and cadherin/catenin function, BioEssays, vol.131, issue.10, pp.883-891, 1997.
DOI : 10.1002/bies.950191008

J. Galan and D. Zhou, Striking a balance: Modulation of the actin cytoskeleton by Salmonella, Proceedings of the National Academy of Sciences, vol.97, issue.16, pp.8754-8761, 2000.
DOI : 10.1073/pnas.97.16.8754

J. Patel and J. Galan, Manipulation of the host actin cytoskeleton by Salmonella ??? all in the name of entry, Current Opinion in Microbiology, vol.8, issue.1, pp.10-15, 2005.
DOI : 10.1016/j.mib.2004.09.001

E. Neer, C. Schmidt, R. Nambudripad, and T. Smith, The ancient regulatory-protein family of WD-repeat proteins, Nature, vol.371, issue.6495, pp.297-300, 1994.
DOI : 10.1038/371297a0

T. Smith, C. Gaitatzes, K. Saxena, and E. Neer, The WD repeat: a common architecture for diverse functions, Trends in Biochemical Sciences, vol.24, issue.5, pp.181-185, 1999.
DOI : 10.1016/S0968-0004(99)01384-5

D. Li and R. Roberts, Human Genome and Diseases:??WD-repeat proteins: structure characteristics, biological function, and their involvement in human diseases, Cellular and Molecular Life Sciences, vol.58, issue.14, pp.2085-2097, 2001.
DOI : 10.1007/PL00000838

Y. Zhang, W. Higashide, S. Dai, D. Sherman, and D. Zhou, Recognition and Ubiquitination of Salmonella Type III Effector SopA by a Ubiquitin E3 Ligase, HsRMA1, Journal of Biological Chemistry, vol.280, issue.46, pp.38682-38688, 2005.
DOI : 10.1074/jbc.M506309200

G. Lotz, A. Brychzy, S. Heinz, and W. Obermann, A novel HSP90 chaperone complex regulates intracellular vesicle transport, Journal of Cell Science, vol.121, issue.5, pp.717-723, 2008.
DOI : 10.1242/jcs.015610

P. Csermely, T. Schnaider, C. Soti, Z. Prohászka, and G. Nardai, The 90-kDa Molecular Chaperone Family, Pharmacology & Therapeutics, vol.79, issue.2, pp.129-168, 1998.
DOI : 10.1016/S0163-7258(98)00013-8