The analysis of cellular transcriptional response at the genome level: Two case studies with relevance to bacterial pathogenesis

Microarray Technology Through Applications

Volumn , Issue , 2007, Pages 125-154

  Carzaniga, Thomas ^a   Sarti, Donatella ^b   Trevino, Victor ^b   Buckley, Christopher ^b   Salmon, Mike ^b   Moobed, Shabnam ^c   Wild, David ^c   Constantinidou, Chrystala ^b   Hobman, Jon L ^b   Dehò, Gianni ^a   Falciani, Francesco ^b  

^a UNIVERSITY OF MILAN   (Italy)

^b UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^c KECK GRADUATE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 81255214081     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (33)

1. Amartey JK, Parhar RS, al-Sedair ST (1997) The effect of antibodies against cell-surface adhesion molecules (LFA-1 alpha and ICAM-1) on the migration and localization of 99mTc-labeled leukocytes in acute infection. Nucl Med Biol 24: 603-605.
2. Anfosso F, Bardin N, Vivier E, Sabatier F, Sampol J, Dignat-George F (2001) Outsidein signaling pathway linked to CD146 engagement in human endothelial cells. J Biol Chem 276: 1564-1569.
3. Baldwin DN, Vanchinathan V, Brown PO, Theriot JA (2003) A gene-expression program reflecting the innate immune response of cultured intestinal epithelial cells to infection by Listeria monocytogenes. Genome Biol 2003:4:R2 Epub 2002.
4. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R (2005) NCBI GEO: mining millions of expression profiles - database and tools. Nucleic Acids Res 33(Database issue): D562-566.
5. Beissbarth T, Speed TP (2004) GOstat: find statistically overrepresented gene ontologies within a group of genes. Bioinformatics 20: 1464-1465.
6. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate-a practical and powerful approach to multiple testing. J R Stat Soc B-Methods 57: 289-300.
7. Boldrick JC, Alizadeh AA, Diehn M, Dudoit S, Liu CL, Belcher CE, Botstein D, Staudt LM, Brown PO, Relman DA (2002) Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci USA 99: 972-977.
8. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics 19: 185-193.
9. Bowen MA, Bajorath J, Siadak AW, Modrell B, Malacko AR, Marquardt H, Nadler SG, Aruffo A (1996) The amino-terminal immunoglobulin-like domain of activated leukocyte cell adhesion molecule binds specifically to the membrane-proximal scavenger receptor cysteine-rich domain of CD6 with a 1:1 stoichiometry. J Biol Chem 271: 17390-17396.
10. Cenni V, Sirri A, De Pol A, Maraldi NM, Marmiroli S (2003) Interleukin-1-receptorassociated kinase 2 (IRAK2)-mediated interleukin-1-dependent nuclear factor kB transactivation in Saos2 cells requires the Akt/protein kinase B kinase. Biochem J 376: 303-311.
11. Conesa A, Nueda MJ, Ferrer A, Talon M (2006) maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics 22: 1096-1102 (e-pub 15 February 2006).
12. Cox JM, Clayton CL, Tomita T, Wallace DM, Robinson PA, Crabtree JE (2001) cDNA array analysis of cag pathogenicity island-associated Helicobacter pylori epithelial cell response genes. Infect Immun 69: 6970-6980.
13. Detweiler CS, Cunanan DB, Falkow S (2001) Host microarray analysis reveals a role for the Salmonella response regulator phoP in human macrophage cell death. Proc Natl Acad Sci USA 98: 5850-5855.
14. Dopazo J, Zanders E, Dragoni J, Amphlett G, Falciani F (2001) Methods and approaches in the analysis of gene expression data. J Immunol Methods 250: 93-112.
15. Eriksson S, Lucchini S, Thompson A, Rhen M, Hinton JC (2003) Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica. Mol Microbiol 47: 103-118.
16. Garnotel R, Rittie L, Poitevin S, Monboisse JC, Nguyen P, Potron G, Maquart FX, Randoux A, Gillery P (2000) Human blood monocytes interact with type I collagen through alpha x beta 2 integrin (CD11c-CD18, gp150-95). J Immunol 164: 5928-5934.
17. Graumann PL, Marahiel MA (1998) A superfamily of proteins that contain the coldshock domain. Trends Biochem Sci 23: 286-290.
18. Gualerzi CO, Giuliodori AM, Pon CL (2003) Transcriptional and post-transcriptional control of cold-shock genes. J Mol Biol 331: 527-539.
19. Lee YK, Puong KY (2002) Competition for adhesion between probiotics and human gastrointestinal pathogens in the presence of carbohydrate. Br J Nutr 88(suppl 1): S101-S108.
20. Ly DP, Zazzali KM, et al. (2003) De novo expression of the integrin alpha5beta1 regulates alphavbeta3-mediated adhesion and migration on fibrinogen. J Biol Chem 278: 21878-21885.
21. Narberhaus F (1999) Negative regulation of bacterial heat shock genes. Mol Microbiol 31: 1-8.
22. Raivio TL, Silhavy TJ (2001) Periplasmic stress and ECF sigma factors. Annu Rev Microbiol 55: 591-624.
23. Sauvonnet N, Pradet-Balade B, et al. (2002) Regulation of mRNA expression in macrophages after Yersinia enterocolitica infection. Role of different Yop effectors. J Biol Chem 277: 25133-25142.
24. Stekel DJ (2003) Microarray Bioinformatics. Cambridge University Press, Cambridge.
25. Stekel DJ, Sarti D, Trevino V, Zhang L, Salmon M, Buckley CD, Stevens M, Pallen MJ, Penn C, Falciani F (2005) Analysis of host response to bacterial infection using error model based gene expression microarray experiments. Nucleic Acids Res 33: e53.
26. Tai YC, Speed TP (2005) Statistical analysis of microarray time course data. In: DNA Microarrays (ed U. Nuber). BIOS Scientific Publishers, Oxford, chapter 20.
27. Takahashi M, Taguchi H, Yamaguchi H, Osaki T, Komatsu A, Kamiya S (2004) The effect of probiotic treatment with Clostridium butyricum on enterohemorrhagic E. coli O157:H7 infection in mice. FEMS Immunol Med Microbiol 41: 219-226.
28. Talaat AM, Lyons R, Howard ST, Johnston SA (2004) The temporal expression profile of Mycobacterium tuberculosis infection in mice. Proc Natl Acad Sci USA 101: 4602-4607.
29. Vaquerizas JM, Conde L, Yankilevich P, Cabezon A, Minguez P, Diaz-Uriarte R, Al- Shahrour F, Herrero J, Dopazo J (2005) GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res 33: W616-W620.
30. Voravuthikunchai S, Lortheeranuwat A, Jeeju W, Sririrak T, Phongpaichit S, Supawita T (2004) Effective medicinal plants against enterohemorrhagic E. coli O157:H7. J Ethnopharmacol 94: 49-54.
31. Weber MHW, Marahiel MA (2003) Bacterial cold shock responses. Sci Prog 86: 9-75.
32. Xia B, Ke H, Inouye M (2001) Acquirement of cold sensitivity by quadruple deletion of the cspA family and its suppression by PNPase S1 domain in Escherichia coli. Mol Microbiol 40: 179-188.
33. Zhang FX, Kirschning CJ, Mancinelli R, Xu XP, Jin Y, Faure E, Mantovani A, Rothe M, Muzio M, Arditi M (1999) Bacterial lipopolysaccharide activates nuclear factor-kappaB through interleukin-1 signaling mediators in cultured human dermal endothelial cells and mononuclear phagocytes. J Biol Chem 274: 7611-7614.