# 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)

![](/files/2Q3ZtfNGxlP5j1AiGfRY)

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

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

![](/files/K1pK57q0a4l7ZU0XCyjD)

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](/partek-genomics-suite/user-manual/visualizations/dot-plot.md). 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.

![](/files/NFyB8SLignDNjmTJ1ngQ)

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 (![](/files/Cihalc0bmcfOAS4occN6))
* Select the **Axes** tab
* Select **Set Cutoff Lines** (Figure 4)

![](/files/tdiUQcQsS5sVWNde6Ims)

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)

![](/files/bBUVH05IDUfMj8YVNl2z)

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).

![](/files/x1GjuqepevztmcaWB4I5)

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.

* Select the upper right-hand quadrant of the volcano plot
* Right click the selected quadrant
* Select **Create List** (Figure 7)

![](/files/JWGXak0CqTxZwjUwaBeq)

Figure 7. Creating a gene list from a volcano plot

* Give the new list a name and description as appropriate
* Select **OK**

The list will be saved as a text file and open as a child spreadsheet in the *Analysis* tab.

## Additional Assistance

If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.


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