This page contains supplementary material for our High-Throughput GoMiner paper.
It has been reported that Mcp-/- mice are unable to mount type 2 helper cell (TH2) responses . Lymph node cells from immunized Mcp-/- mice synthesize extremely low levels of interleukin-4, interleukin-5, and interleukin-10 but normal amounts of interferon-gamma and interleukin-2. Consequently, those mice do not accomplish the immunoglobulin subclass switch. Gu et al.  have concluded that MCP1 influences both innate immunity (through effects on monocytes) and adoptive immunity (through control of T-helper cell polarization). The defective humoral immunity in the CVID patient may have been caused in part by a skewed response of T cell help away from the TH2 pathway toward the TH1 pathway. That possibility is reflected in the low expression of chemokine CCL2 (also named monocyte chemotactic protein 1, or MCP1), which is present in almost all of the significant categories (Figure 3 - see paper).
PTPNS1 (MYD1), a dendritic cell surface antigen, has been reported to affect activation of T lymphocytes . The low expression of PTPNS1 (Figure 3 - see paper), which is present in only the �cell adhesion� category (enrichment = 3.3; p= 10-2.1; FDR = 0.01), may be associated with impaired CD4+ T cell activation during the immune response.
The underexpressed gene HLA-DRA is a member of a number of important categories including �antigen presentation� (enrichment = 12.8; p = 10-2.0; FDR = 0.10), �antigen processing� (enrichment = 12.8; p = 10-2.0; FDR = 0.10), �defense response� (enrichment = 3.2; p = 10-4.8; FDR = not detectable), and �immune response� (enrichment = 3.4; p = 10-5.1; FDR = not detectable), as indicated in Figure 3 (see paper) and Gene Category Report. HLA-DRA is an MHC class II gene. MHC class II genes are critical for antigen recognition by the immune system, and absence of constitutive and inducible MHC class II gene expression causes severe combined immunodeficiency (SCID) . The absence of HLA-DRA may contribute to the phenotype of CVID in some patients [4-6].
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