Fig. 3: Dynamic proteomics profiling.

a The four clusters of proteins with different expression dynamics for the SC and LC groups computed with Mfuzz analysis (one-way ANOVA, B-H adjusted P-value < 0.05, more details in Supplementary Table S2b). b–d Pathways enrichment by ingenuity pathway analysis (IPA) for the proteins in Clusters 1, 2, and 4 of the SC and LC groups. e–g Heatmaps showing the unique proteins of the SC and LC groups in Clusters 1, 2, and 4 (more details in Supplementary Table S2b), as well as the corresponding top two pathways annotated by IPA (P-value < 0.05). Proteins highlighted in red are discussed in the main text. h Pathways enriched by IPA (P-value < 0.05) across the nine weeks (no pathways were enriched for the 3rd, 5th, or 9th weeks) using the differentially expressed proteins between the LC and SC groups (Supplementary Table S2d). The z-score represents the activation state of the pathways: z-score > 0 means the pathway is active, while z-score < 0 indicates that the pathway is inhibited. i The relationship between LXR/RXR and their downstream proteins which uniquely belong to the LC (lipid metabolism-associated proteins) and SC (inflammation response-associated proteins) groups in Cluster 1 (a). Blue: downregulated proteins/metabolites in the LC group at the 1st week; red: upregulated proteins/metabolites in the LC group at the 1st week; gray: no significantly different molecules were found between the two groups at the 1st week. The interactions retrieved from STRING are visualized with Cytoscape.