Detection of gene expression in an individual cell type within a cell mixture using microarray analysis

PLoS ONE

Volumn 4, Issue 2, 2009, Pages

  Bryant, Penelope A ^a,b   Smyth, Gordon K ^c   Robins Browne, Roy ^a,b   Curtis, Nigel ^a,b  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b ROYAL CHILDREN'S HOSPITAL   (Australia)

^c WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL CULTURE; CELL FRACTIONATION; CELL INTERACTION; CELL ISOLATION; CELL SELECTION; CELL TYPE; COMPARATIVE STUDY; CONTROLLED STUDY; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC CORRELATION; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; MONOCYTE; PERIPHERAL BLOOD MONONUCLEAR CELL; QUANTITATIVE ANALYSIS; RNA HYBRIDIZATION;

EID: 84887212491     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0004427     Document Type: Article

References (25)

1. 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 U S A 98: 5850-5855.
2. Huang Q, Liu D, Majewski P, Schulte LC, Korn JM, et al. (2001) The plasticity of dendritic cell responses to pathogens and their components. Science 294: 870-875.
3. Skelton L, Cooper M, Murphy M, Platt A (2003) Human immature monocytederived dendritic cells express the G protein-coupled receptor GPR105 (KIAA0001, P2Y14) and increase intracellular calcium in response to its agonist, uridine diphosphoglucose. J Immunol 171: 1941-1949.
4. Viemann D, Schulze-Osthoff K, Roth J (2005) Potentials and pitfalls of DNA array analysis of the endothelial stress response. Biochim Biophys Acta 1746: 73-84.
5. Boldrick JC, Alizadeh AA, Diehn M, Dudoit S, Liu CL, et al. (2002) Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci U S A 99: 972-977.
6. Bolt G, Berg K, Blixenkrone-Moller M (2002) Measles virus-induced modulation of host-cell gene expression. J Gen Virol 83: 1157-1165.
7. Rus V, Atamas SP, Shustova V, Luzina IG, Selaru F, et al. (2002) Expression of cytokine- and chemokine-related genes in peripheral blood mononuclear cells from lupus patients by cDNA array. Clin Immunol 102: 283-290.
8. Asano T, McWatters A, An T, Matsushima K, Kleinerman ES (1994) Liposomal muramyl tripeptide up-regulates interleukin-1 alpha, interleukin-1 beta, tumor necrosis factor-alpha, interleukin-6 and interleukin-8 gene expression in human monocytes. J Pharmacol Exp Ther 268: 1032-1039.
9. Baqui AA, Jabra-Rizk MA, Kelley JI, Zhang M, Falkler WA Jr, et al. (2000) Enhanced interleukin-1beta, interleukin-6 and tumor necrosis factor-alpha production by LPS stimulated human monocytes isolated from HIV+ patients. Immunopharmacol Immunotoxicol 22: 401-421.
10. Guha M, Mackman N (2001) LPS induction of gene expression in human monocytes. Cell Signal 13: 85-94.
11. DeForge LE, Remick DG (1991) Kinetics of TNF, IL-6, and IL-8 gene expression in LPS-stimulated human whole blood. Biochem Biophys Res Commun 174: 18-24.
12. Tridandapani S, Lyden TW, Smith JL, Carter JE, Coggeshall KM, et al. (2000) The adapter protein LAT enhances fcgamma receptor-mediated signal transduction in myeloid cells. J Biol Chem 275: 20480-20487.
13. Fessele S, Boehlk S, Mojaat A, Miyamoto NG, Werner T, et al. (2001) Molecular and in silico characterization of a promoter module and C/EBP element that mediate LPS-induced RANTES/CCL5 expression in monocytic cells. Faseb J 15: 577-579.
14. Leoni F, Zaliani A, Bertolini G, Porro G, Pagani P, et al. (2002) The antitumor histone deacetylase inhibitor suberoylanilide hydroxamic acid exhibits anti-inflammatory properties via suppression of cytokines. Proc Natl Acad Sci U S A 99: 2995-3000.
15. Lu M, Zhang M, Takashima A, Weiss J, Apicella MA, et al. (2005) Lipopolysaccharide deacylation by an endogenous lipase controls innate antibody responses to Gram-negative bacteria. Nat Immunol 6: 989-994.
16. Holloway AJ, Oshlack A, Diyagama DS, Bowtell DD, Smyth GK (2006) Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis. BMC Bioinformatics 7: 511.
17. Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162: 156-159.
18. Yang YH, Buckley MJ, Dudoit S, Speed TP (2002) Comparison of methods for image analysis on cDNA microarray data. Journal of Computational and Graphical Statistics 11: 108-136.
19. Smyth GK (2005) Limma: linear models for microarray data. In: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W, eds. Bioinformatics and Computational Biology Solutions using R and Bioconductor. New York: Springer. pp 397-420.
20. Smyth GK, Speed T (2003) Normalization of cDNA microarray data. Methods 31: 265-273.
21. Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3: Article 3.
22. Smyth GK, Michaud J, Scott HS (2005) Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 21: 2067-2075.
23. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B 57: 289-300.
24. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95: 14863-14868.
25. Beissbarth T, Speed TP (2004) GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 20: 1464-1465.