Abstract
Microarray technology can rapidly generate large databases of gene expression profiles. Our laboratory has applied these techniques to analyze differential gene expression in cardiac tissue and cells based on mouse heart transplantation. We have analyzed the different gene expression profiles such as stress or injury including ischemia following transplantation. We also have investigated the role of infiltrating inflammatory cells during graft rejection by purifying subsets of infiltrating cells using GFP transgenic mice and detailed all technical experiences and issues. The purpose of this study is to assist researchers to simplify the process of analyzing large database using microarray technology.
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References
Christopher, K., Mueller, T. F., Ma, C., Liang, Y., and Perkins, D. L. (2002) Analysis of the innate and adaptive phases of allograft rejection by cluster analysis of transcriptional profiles. J. Immunol. 169, 522–530.
Christopher, K., Mueller, T. F., DeFina, R., et al. (2003) The graft response to transplantation: a gene expression profile analysis. Physiol. Genomics 15, 52–64.
DeFina, R. A., Liang, Y., He, H., et al. (2004) Analysis of immunoglobulin and T-cell receptor gene deficiency in graft rejection by gene expression profiles. Transplantation 77, 580–586.
Liang, Y., Christopher, K., DeFina, R., et al. (2003) Analysis of cytokine functions in graft rejection by gene expression profiles. Transplantation 76, 1749–1758.
He, H., Stone, J. R., and Perkins, D. L. (2002) Analysis of robust innate immune response after transplantation in the absence of adaptive immunity. Transplantation 73, 853–861.
Corry, R. J., Winn, H. J., and Russell, P. S. (1973) Heart transplantation in congenic strains of mice. Transplant. Proc. 5, 733–735.
McKee, C. M., Defina, R., He, H., Haley, K. J., Stone, J. R., and Perkins, D. L. (2002) Prolonged allograft survival in TNF receptor 1-deficient recipients is due to immunoregulatory effects, not to inhibition of direct antigraft cytotoxicity. J. Immunol. 168, 483–489.
Brazma, A., Hingamp, P., Quackenbush, J., et al. (2001) Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nat. Genet. 29, 365–371.
Eisen, J. S. (1998) Genetic and molecular analyses of motoneuron development. Curr. Opin. Neurobiol. 8, 697–704.
Zhang, X., Lu, X., Shi, Q., et al. (2006) Recursive SVM feature selection and sample classification for mass-spectrometry and micrarray data. BMC Bioinformatics 7, 197.
Castillo-Davis, C. I. and Hartl, D. L. (2003) Gene Merge—post-genomic analysis, data mining, and hypothesis testing. Bioinformatics 19, 891–892.
Tseng, G. C. and Wong, W. H. (2005) Tight clustering: a resampling-based approach for identifying stable and tight patterns in data. Biometrics 61, 10–16.
Liu, X., Brutlag, D. L., and Liu, J. S. (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 127–138.
Liu, X. S., Brutlag, and Liu, J. S. (2002) An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20, 835–839.
Liu, Y., Wei, L., Batzoglou, S., Brutlag, D. L., Liu, J. S., and Liu, X. S. (2004) A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Res. 32, W204–207.
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Liang, Y., Lu, X., Perkins, D.L. (2007). Microarray Analysis of Gene Expression in Murine Cardiac Graft Infiltrating Cells. In: Zhang, J., Rokosh, G. (eds) Cardiac Gene Expression. Methods in Molecular Biology, vol 366. Humana Press. https://doi.org/10.1007/978-1-59745-030-0_1
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DOI: https://doi.org/10.1007/978-1-59745-030-0_1
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