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Fig. 6 | BMC Biology

Fig. 6

From: Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

Fig. 6

The iTreg subnetwork is linked to common autoimmune diseases. The selected iTreg subnetwork (see Fig. 5) was tested for connection with diseases using multiple public sources of annotation. a, b The enrichment of the GWAS catalog disease categories in addition to two categories of autoimmune diseases (Ai6 and Ai21, see Results text) is shown. For each category, the null distribution of the odds ratios (ORs) obtained with 10,000 random gene sets from the full network is shown as a histogram and the observed OR with a vertical red line. The categories in bold have a resampling-based p value of < 0.05. The resampled OR null distribution was used to calculate a FWER using the step-down minimum p value procedure. Enrichment in PPI modules is shown for categories with a nominal p value of < 0.05 (Fisher’s exact test), and 119 hypotheses were tested. The modules from a PPI network are given for the corresponding enriched categories and three PPI modules associated to the top three enriched in iTreg subnetwork disease categories are displayed in (b). Light blue nodes correspond to genes with an associated SNP in the GWAS catalog. c The treemap shows the enrichment p values of the indicated Open Target categories for the iTreg subnetwork. Only disease associations with nominal p < 0.05 are shown. The size of the square is proportional to the –log10(p) and disease types are grouped by therapeutic areas. d Gene Set Enrichment Analysis (see Methods) confirms that the iTreg subnetwork gene set is positively enriched in the ranked list obtained when comparing gene expression in CD4+ T cells from gastrointestinal tissue or blood of inflammatory bowel disease patients (UC or CD as indicated) or from cerebrospinal fluid (CSF) of MS patients compared to controls. CTRL: control, symptomatic or healthy; OND: other neurological disease; ES: enrichment score

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