Fig. 5: Proteomic analysis in the cerulein-induced CP model.

A Principal component analysis (PCA) of all samples based on their proteomic profiles, displayed in various colors to differentiate experimental groups (n numbers as in Fig. 4: n = 6 for all groups, except for the CP Navi group with n = 7). B Percentage of differentially expressed proteins identified based on at least two peptides. Comparisons were conducted using Student’s t-test followed by permutation-based false discovery rate (FDR) correction (q-value < 0.05). A minimum of four valid label-free quantification (LFQ) intensity values in at least one of the two tested groups were required for each test. C Box plot depicting the distribution of collagen protein intensities across different experimental groups. The average log2-transformed LFQ intensity values for collagen proteins (COL1A1, COL1A2, COL3A1, COL4A1, COL4A2, COL5A1, COL5A2, COL6A1, COL6A2, COL6A5, COL6A6, COL12A1, COL14A1, COL15A1, COL18A1) were calculated and plotted within each group. D The average levels of proteins S100A8 and S100A9 in different experimental groups. Mean values were calculated from log2-transformed LFQ intensities. Both proteins were not quantified in the Sham group. Results are presented as mean values. Statistical analysis was performed using Student’s t-test. *q  < 0.05; ***q  < 0.001. Statistical significance indicated in the graph applies to both proteins analyzed. E Gene Ontology (GO) analysis of Cellular Component enrichment for proteins upregulated (fold change ≥ 2.0) in the CP Navi vs. CP comparison. F GO analysis of Cellular Component enrichment for proteins downregulated (fold change ≥ 2.0) in the CP Navi vs. CP comparison. G GO analysis of Cellular Component enrichment for proteins upregulated (fold change ≥ 1.2) in the CP Ven vs. CP comparison. H GO analysis of Cellular Component enrichment for proteins downregulated (fold change ≥ 1.2) in the CP Ven vs. CP comparison. Analyses in (E–H) were performed using ShinyGO v0.82 [62].