The volcano plot is a special 2-D scatter plot used to visualize significance and the magnitude of changes in features (e.g. genes or transcripts) within a given comparison. By convention, the X-axis represents the fold change between the two groups and is on a log₂ scale.  On the other hand, the Y-axis shows the p-values from the statistical test of the comparison and it is on a log₁₀ scale.

As a prerequisite for invoking the volcano plot, you must run a Differential gene expression analysis. When setting-up the analysis, include all relevant contrasts you would like to view the volcano plots for.

Once the analysis is complete, open the resulting Feature list data node. Navigate to the Gene list section of the page and click on the volcano plot icon, located above the header of a Fold change column (Figure 1).  

 

Each point on the plot represents the statistical result for a single gene, transcript or feature. The color of the point reflects fold change: genes with a fold change above 2 (up-regulated) are in green, genes with a fold change below -2 (down-regulated) are in red. The remaining genes are in grey (Figure 2). The plot header is derived from the name of the contrast.

Thick vertical lines representing fold changes of -2 and +2 are highlighted. A thick horizontal line represents a p-value of 0.05. The number of genes that are up/downregulated by at least 2 and have a p-value less than 0.05 are listed at the lower left corner of the plot.

 

 

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