Fig. 3

RNA-sequencing analysis of the molecular implications associated with the inflammatory bowel disease (IBD)-like phenotype in ctla-4-/- zebrafish. (A) Heatmap of differentially expressed genes between the intestines from wild-type (WT) and ctla-4-/- zebrafish. (B) Volcano plot showing the up-/down-regulated genes in the intestines of ctla-4-/- zebrafish compared with those of WT zebrafish. Red represents up-regulated genes, while blue denotes down-regulated genes. (C) GO analysis showing top 10 terms in biological processes of differentially expressed genes (DEGs). (D) GO analysis showing top 10 terms in biological processes of all up-regulated genes. (E) Heatmap showing row-scaled expression of the representative differently expressed inflammation and chemotaxis-related genes. (F) The mRNA expression levels of important genes associated with inflammation and chemokines confirmed by real-time qPCR. (G) Protein-protein interaction network was constructed using the DEGs. The nodes represent the proteins (genes); the edges represent the interaction of proteins (genes). (H) The myeloperoxidase (MPO) activity in the intestines (up) and peripheral blood (down). (I) Heatmap showing row-scaled expression of the IBD biomarker genes and IBD-related genes. (J) The mRNA expression levels of representative IBD biomarker genes and IBD-related genes were analyzed by real-time qPCR. Data are presented as mean ± standard deviation (SD). Statistical significance was assessed through an unpaired Student’s t-test (**p < 0.01; ***p < 0.001; ****p < 0.0001).