Proteomic Signatures of Human Visceral and Subcutaneous Adipocytes

Figures

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  Figure 1.. Global proteome GO term enrichment. GO enrichment analysis of all identified proteins (n = 2939) in the SA and VA adipocytes. The enrichment analysis was retrieved using ClueGO limited to top 2 GO term levels for biological processes (BP), cellular components (CC), and molecular function (MF). The figure shows the percentage of associated genes from the adipocyte proteome represented by significantly enriched GO terms (adj. P value < 0.05). The GO terms are sorted from the most significant on top to less significant on the bottom for each GO term group, respectively.

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  Figure 2.. Global correlation map of SA and VA proteome. The global correlation maps show cross-correlations of all quantified proteins using Pearson correlation coefficient and subsequent unsupervised hierarchical clustering for a) SA and b) VA proteome, respectively. This analysis revealed extensive maps of co-regulated proteins in respective clusters. In the map, proteins with a strong correlation or anti-correlation to each other cluster together in red or blue areas, respectively. The protein lists of the main correlation clusters were submitted to ClueGO enrichment analysis of biological processes (BP), and cellular components (CC). The most significantly enriched terms of 2 cluster levels can be found on the right from the maps.

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  Figure 3.. SA and VA GO term enrichment. GO enrichment analysis of all significantly upregulated SA (n = 576) and VA (n = 564) proteins. The enrichment analysis was retrieved using ClueGO with a significance threshold of 0.05 and merging all redundant groups with > 50% overlap for a) cellular components (CC), b) biological processes (BP), and c) molecular function (MF). The figure shows the most significantly enriched GO terms (adj. P value < 0.05) for SA, and VA upregulated proteins, respectively.

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  Figure 4.. Pathway and reaction analysis of differentially expressed proteins. Reactome pathway and reactions enrichment analysis of all significantly a) SA and b) VA upregulated proteins. Figures show the most significant terms (P values < 0.05) using the Reactome build-in Voronoi diagram visualization tool. The terms are visualized based on the Reactome event hierarchy showing the most significant terms in bright yellow.

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  Figure 5.. SA and VA upregulated proteins pathway and interaction analysis. The figure shows the most significant Reactome pathways and reactions (P values < 0.05) together with associated proteins and protein-protein STRING interaction links visualized using Cytoscape GlueGO+CluePedia plugin. SA and VA Reactome pathway and reaction term nodes are shown as red and blue circles, respectively. The size of the nodes indicates the significance of the node—the bigger, the more significant. Related terms connect edges of a gray color. Nodes sharing upregulated proteins of both groups are transparent. Bright red and green edges indicate the ability of the protein to activate or inhibit the coupled protein. The most significant terms of each cluster group were visualized and manually adjusted to obtain a reader-friendly pathway network. All pathways and networks with group cluster affiliation are accessible in Supplemental File 4 (29).

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  Figure 6.. The most differentially expressed proteins. a) Volcano plot for differential protein expression analysis showing the top 20 most upregulated proteins of SA (green) and VA (red). b) Protein abundance rank of the most differentially expressed proteins. The mean intensity values of all measured proteins were ordered from the larger to the lowest values and ranked accordingly. The plot shows the relative representation of the most differentially expressed proteins within the whole adipocyte proteome. c) The box plot shows the differences between SA and VA intensity values of the most differentially expressed proteins. Cross stands for imputed values and dot for experimental intensity values.

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  Figure 7.. SA module-trait relationships. SA module-trait relationship and corresponding P values (Pearson) between the module eigengenes and selected clinical traits. Strong positive correlations are in red, while strong negative correlations are blue, numbers in individual cells are correlation coefficient (P value). Significant module-trait correlations (P < 0.05) with the absolute correlation value >0.5 are in bold. The size of the modules is in brackets. Waist1 stands for the waist circumference measured at the inferior margin of the ribs, and waist2 measured at the umbilical level.

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  Figure 8.. VA module-trait relationships. VA module-trait relationship and corresponding P values (Pearson) between the module eigengenes and selected clinical traits. Strong positive correlations are in red, while strong negative correlations are blue, numbers in individual cells are correlation coefficient (P value). Significant module-trait correlations (P < 0.05) with the absolute correlation value > 0.5 are in bold. The size of the modules is in brackets. Waist1 stands for the waist circumference measured at the inferior margin of the ribs, and waist2 measured at the umbilical level.