Fig. 1

The core genes and pathways of newly diagnosed treatment-naive pediatric Ulcerative colitis emphasize lymphocyte activation and mitochondrial dysfunction. a Volcano plot of the 5296 differentially expressed genes between 206 UC and 20 Ctl samples (FC ≥ 1.5 and FDR < 0.001). Functional annotation enrichment analyses of the b 3600 upregulated and c 1696 downregulated UC core genes using CluGO⁸ charts. Detailed functional annotation enrichment analyses of the d 3600 upregulated and e 1696 downregulated UC core genes using ToppGene⁶, ToppCluster⁷, and Cytoscape⁵² are shown. GO Biological Process, Cellular Component, and Molecular Function (pink), pathways (light blue), mouse phenotype (blue), gene family (yellow), coexpression (light green), disease (dark green), interactions (purple). The full list of gene set enrichment results and P values are in Supplementary Dataset 1. f Computational deconvolution of cell subset proportions in 206 UC and 20 controls. Differences (Wilcoxon test with FDR < 0.01 (**)) are shown for cell types with at least 80% non-zero values. Overlap of differentially expressed genes between UC and Ctl in g RISK, h isolated colon epithelial cells (IEC¹³), and i a microarray study of adult cases (GSE59071 ¹²). j Detailed functional annotation enrichment analyses of the shared downregulated functions of the above studies. Box and whisker plot with central line indicating median, box ends representing upper and lower quartile, and whisker represent 10–90 percentile. UC ulcerative colitis