Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells

Figure 5

GM-CSF-positive CD4 T cell signatures are associated with autoimmune diseases, especially MS. (a) Gene set enrichment analysis is shown using genes ranked by the – function, and the Open Targets database [68] was used to provide gene sets associated with diseases. NES: normalized enrichment score; pval: value; padj: FDR. (b) The heat map represents the row-scaled expression values from RNA-seq data of CD4 T cells from MS patients or healthy controls (data from [26]). Groups are separated based on disease status (MS or healthy) and myelin antigen reactivity (reactive: tetramer+). Genes are selected as those identified in the current RNA-seq study as differentially expressed between GM-CSF-positive versus GM-CSF-negative cells and having detectable expression in at least 4 samples in the data from [26]. (c) Of the 110 established non-MHC MS susceptibility variants [70], two SNPs mapped to consensus peaks from the current ATAC-seq study. Information about these SNPs is shown in the table, along with the differential accessibility analysis in GM-CSF-positive versus GM-CSF-negative CD4 T cells.

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