Fig. 3: Functional analyses of the dysregulated proteins.

a, b Differentially expressed proteins (DEPs) are shown in the volcano plots: a pediatric malignant nodules (PM) vs. pediatric benign nodules (PB) and b PM vs. adult malignant nodules (AM). The cutoff is defined by requiring the fold change (FC) to be greater than 1.5, with adjusted P < 0.05 (BH-adjusted two-sided Welch’s t test). The names of the up/downregulated proteins with the top five largest FC are reported in the plots. c The scatter diagram shows the FC distribution of the dysregulated proteins in two pairwise comparisons: PM vs. PB and PM vs. AM. The overlapping significantly co-dysregulated proteins are colored in red. The proteins significantly dysregulated in PM/PB are colored in orange, and those dysregulated in PM/AM are colored in blue. Here, the DEP lists were derived from FC threshold 1.5. d The heatmap shows 37 proteins: they are co-upregulated/co-downregulated proteins and the five most up-/down- regulated ones from the volcano plots (a, b). Proteins were clustered using hierarchical clustering. e Pathway enrichment of the 243 DEPs from the volcano plot with the PM/PB comparisons (FC > 1.5). The red and blue bars represent the active and inhibited pathways, respectively. f Results of the gene ontology enrichment of the biological processes using the DEPs in PM/PB. g Pathway enrichment of 121 DEPs from the volcano plot with the PM/AM comparisons (FC > 1.5). The red and blue bars represent the active and inhibited pathways, respectively. P values are derived from one-sided Fisher’s Exact Test for pathway and gene ontology enrichment.