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. 2024 Jan 22;12:RP88732. doi: 10.7554/eLife.88732

Figure 3. Integrative analysis of transcriptome, proteome, and phosphoproteome.

Figure 3.

(A) Circos plot of gene expression at different levels from transcription, to protein, and to phosphorylation. Bars in each layer of circle represent changes in significantly regulated molecules (q-value or p-value <0.05) in transcriptome, total proteome, and unnormalized phosphoproteome. Bar height, color, and direction represent log2(fold change). Red and upward indicate upregulation, and blue and downward indicate downregulation. (B–C) Scatter plots of correlation between phosphoproteome and transcriptome (B) or total proteome (C). (D) Comparison of canonical pathway enrichments from the transcriptome, total proteome, and phosphoproteome. Enrichment z-scores were calculated in IPA, and were scaled to generate heatmap in R language. (E) Integrative graph of expression of all phosphoproteins and selected types of molecules. Bar plot on the bottom displays expression of all significantly changed (p-value <0.05) phosphoproteins in unnormalized phosphoproteome. Y-axis denotes log2(fold change), and x-axis denotes each molecule ranked by log2(fold change). Bars were colored by -log10(p-value). Stick plots on the top display kinases, phosphatases, and transcription factors (TFs) selected from the bottom bar plot and their changes in transcriptome (RNA), total proteome (pro), and normalized phosphoproteome (norm). From top to bottom: each large block denotes the changes of certain types of molecules (from kinases to phosphatases, to TFs). In each block, the three rows from top to bottom indicate the changes in transcriptome, total proteome, and normalized phosphoproteome. Each stick represents a molecule and color represents the change: red: (p-value or q-value <0.05) and log2FC >0; blue: (p-value or q-value <0.05) and log2FC <0; black: (p-value or q-value ≥0.05) or log2FC = 0; gray: unidentified in one of the omics. Their locations are matched to those in the bottom bar plot. (F–J) Pie plots of the composition of phosphoproteins in the unnormalized phosphoproteome. Regardless of p-value, numbers of four types of proteins, including kinases, phosphatases, TFs, and others, are displayed in (F). After filtration with cutoff p-value <0.05, numbers of those types of proteins are displayed in (G). Extracted from G, numbers of upregulated and downregulated kinases (H), phosphatases (I), and TFs (J) are displayed.