How Should Upregulation and Downregulation Be Interpreted in KEGG Bubble Plots?
KEGG bubble plots are a visualization tool used to represent changes in gene expression data within KEGG pathways. Each bubble in the plot corresponds to a specific pathway, with the color and size of the bubble reflecting the changes in gene/protein/metabolite expression within that pathway. This approach aids in understanding the differential roles of genes/proteins/metabolites in biological pathways under varying conditions.
In KEGG bubble plots, upregulation and downregulation of gene expression are typically conveyed through the following visual cues:
Color
The color of each bubble generally indicates whether gene expression is upregulated or downregulated. For instance, red may represent upregulation, green typically indicates downregulation, and blue or gray suggests no statistically significant changes. The exact meaning of each color should be referenced in the figure legend.
Size
The size of the bubble correlates with the magnitude or significance of the gene's effect within the pathway. Larger bubbles typically indicate a more substantial influence of the gene on the pathway or a more significant change in gene expression.
Position
The position of the bubble on the plot may correspond to specific biological pathways or functional categories, helping to group related pathways.
Opacity
In some cases, bubble opacity can be used to denote the significance of the expression change. Lower opacity often indicates less significant changes in gene expression.
By analyzing the color, size, and opacity of the bubbles in a KEGG bubble plot, one can assess the upregulation and downregulation of genes/proteins/metabolites across various pathways under different experimental conditions. However, it is important to note that KEGG bubble plots serve as a preliminary visualization tool. To comprehensively evaluate gene/protein/metabolite expression and their impact on pathways, additional data and more detailed analysis methods are required.
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