Volcano Plot

The volcano plot displays p-values and fold-changes of numerous genomic features (e.g., genes or probe sets) at the same time. This allows differentially expressed genes to be quickly identified and saved as a gene list.

Note: the same list can be generated without a visual aid using the List Manager (ANOVA Streamlined tab).

We will invoke a volcano plot from an ANOVA results child spreadsheet with genes on rows.

Select View from the main toolbar
Select Volcano Plot (Figure 1)

Figure 1. Invoking a volcano plot on an ANOVA results spreadsheet

The Volcano Plot Configure dialog will open (Figure 2).

Figure 2. Select the columns to display in the volcano plot

Select the fold-change and p-value columns you would like to visualize from the ANOVA results spreadsheet; here we have chosen 12. Fold-Change(Down Syndrome vs. Normal) for the X Axis and 10. p-value(Down Syndrome vs. Normal) for Y Axis
Select OK

The volcano plot will open in a new tab (Figure 3). Control and color options for the volcano plot are largely similar to those described for a dot plot. On volcano plots with many probe(sets)/genes, the shapes and sizes of individual probe(sets)/genes will not be visible until they are selected.

Figure 3. The volcano plot shows each probe(set)/gene as a point. The X Axis shows fold change with no change (N/C) as the mid-point. The Y Axis shows p-values in descending value from a maximum of 1 at the X Axis intersection.

To facilitate analysis, we can add cutoff lines for both fold-change and p-value.

Select the Axes tab
Select Set Cutoff Lines (Figure 4)

Figure 4. Adding cutoff lines to the volcano plot

Set Vertical Line(s) to 1.3 and -1.3
Set Horizontal Line(s) to 0.05
Select Select all points in a section
Select OK (Figure 5)

Figure 5. Setting cutoff lines. The vertical lines are fold-change cutoffs. The horizontal line is a p-value cutoff.

Select OK to close the Plot Rendering Properties dialog

The volcano plot now has cutoff lines for fold-change and p-value (Figure 6).

Figure 6. Cutoff lines facilitate visual analysis of ANOVA results

Because we selected Select all points in a section when adding the cutoff lines, selecting any of the quandrants will select all probe(sets)/genes in that quadrant. If this option is not selected, individual probe(sets)/genes or groups can be selected using selection mode. Gene lists can be generated from selected probe(sets)/genes.

If columns are selected in the ANOVA results source spreadsheet for the volcano plot, only those columns will be included in the created list.