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Figure 2 | Genome Medicine

Figure 2

From: Integrated analysis reveals microRNA networks coordinately expressed with key proteins in breast cancer

Figure 2

Effect of mRNA and miRNA on protein expression. (A) The effect of mRNA on protein for all significant mRNA coefficients (‘gamma’). (B) Volcano plot showing all estimated mRNA coefficients (‘gamma’) plotted against corresponding P-values. Significant and negative associations are shown in blue and significant and positive associations are shown in red. (C) The effect of miRNA on protein for all significant miRNA coefficients (‘beta’). (D) Volcano plot showing all estimated miRNA coefficients (‘beta’) plotted against corresponding P-values. Coloring as in (B). (E) Number of miRNAs per protein. The horizontal axis represents the negative and positive number of associations with miRNAs, and the vertical axis represents the 105 proteins in descending order. (F) Number of proteins per miRNA. The horizontal axis represents the negative and positive number of associations with proteins, and the vertical axis represents the 421 miRNAs in descending order. (G) Example of a negative association between miRNA expression and protein expression. The horizontal axis represents BRAF mRNA expression and the vertical axis B-Raf protein expression (both on log2-scale). Each point represents a patient, and the color indicates whether the expression of miR-638 is above the median (red) or below the median (black). Solid lines represent smoothing splines fitted to the data. The dotted line represents a linear regression fit to the data. For any fixed level of mRNA expression, high expression of miR-638 is associated with decreased protein expression of B-Raf. (H) Example of a positive association between miRNA expression and protein expression. The horizontal and vertical axes are the same as in (G), but here each patient point is color-coded according to miR-107 expression (red, miR-107 expression above median; black, miR-107 expression below median). For any fixed level of mRNA expression, high expression of miR-107 is associated with increased B-Raf protein expression.

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