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Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data

Abstract

Immune cell-specific expression is one indication of the importance of a gene's role in the immune response. We have compiled a compendium of microarray expression data for virtually all human genes from six key immune cell types and their activated and differentiated states. Immune Response In Silico (IRIS) is a collection of genes that have been selected for specific expression in immune cells. The expression pattern of IRIS genes recapitulates the phylogeny of immune cells in terms of the lineages of their differentiation. Gene Ontology assignments for IRIS genes reveal significant involvement in inflammation and immunity. Genes encoding CD antigens, cytokines, integrins and many other gene families playing key roles in the immune response are highly represented. IRIS also includes proteins of unknown function and expressed sequence tags that may not represent genes. The predicted cellular localization of IRIS proteins is evenly distributed between cell surface and intracellular compartments, indicating that immune specificity is important at many points in the signaling pathways of the immune response. IRIS provides a resource for further investigation into the function of the immune system and immune diseases.

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Acknowledgements

Kay Dennis, Henry Chiu, Sudeepta Aggarwal, Vandana Chauhan and Fay Wang for sample preparation, Karen Toy, Grazyna Fedorowicz and Rob Soriano for microarray experiments, Thomas Wu, Cynthia Honchell and Mike Ward for microarray analysis tools, Zemin Zhang, Yan Zhang and Shiuh-Ming Luoh for gene annotation tools, Michael Ostland for statistical analysis, Jill Schoenfeld for gene analysis, Dan Eaton and Bernd Wranik for identification of BTLA gene and Allison Bruce for graphics services.

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Correspondence to H F Clark.

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Supplementary information accompanies the paper on Genes and Immunity website (http://www.nature.com/gene).

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Abbas, A., Baldwin, D., Ma, Y. et al. Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data. Genes Immun 6, 319–331 (2005). https://doi.org/10.1038/sj.gene.6364173

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