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.

Haplotypes of the interleukin 7 receptor alpha gene are correlated with altered expression in whole blood cells in multiple sclerosis

“…It is particularly interesting that CD127 expression has been reported to be threefold lower in effector/memory (CD45RO þ ) than naïve T cells (CD45RA þ ), 31 and greatly reduced in Th1 cells compared to resting memory cells. 22 As both CD45RO þ and Th1 cells are large sources of CD127 mRNA in PBMCs, a significant imbalance, with an excess of either or both, might be expected to contribute to the measured reduction in CD127 mRNA in PPMS detected in this study.…”

“…As CD127 expression is very low in neutrophils, 22 and neutrophils account for the majority of mRNA in whole blood, we tested peripheral blood mononucleocytes (PBMC) RNA (that is, neutrophil depleted component), and found that CD127 mRNA expression was still much lower in PPMS (Pp0.003, Figure 2b). The majority of mRNA from PBMCs is from T cells (typically 80%).…”

“…23 B cells and NK cells are typically less than 10%, and produce little CD127 mRNA. 22 Macrophages and monocytes, produce less CD127 mRNA than T cells, and are about 10% of the PBMC fraction. The recapitulation of the measurement of reduced CD127 mRNA in PPMS whole blood in the PBMC fraction comparison indicates that the lymphocyte and monocyte component of whole blood is the likely major source of the observed difference in CD127 mRNA levels.…”

High-density SNP analysis of 642 Caucasian families with rheumatoid arthritis identifies two new linkage regions on 11p12 and 2q33

“…49,53 The data illustrate the striking increase in linkage information that can be obtained by using appropriate SNP linkage panels. Recently, a number of reports have appeared using such panels, with evident success in identifying new regions of linkage.…”

Acute psychological stress induces short-term variable immune response

“…To ensure that genes found significantly differentially expressed post-landing were not solely a consequence of increased proportion of NK cells, we used a multivariate linear model to regress individual gene expression levels against NK-cell specific marker genes. The criteria for classification as a NK-cell marker were that the genes must be these particular genes needed to be: 1) identified in multiple publications linking them to the NK-cell type; and 2) found intersecting across three independent cell type specific expression databases [CTen (Shoemaker et (Miller et al, 2013), we note that the model is fairly robust to choice of marker genes for cell type.…”