# 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)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-032ecde96fbeacb9034314f8c29ec371cb0570b2%2F2017-08-15%2016_53_20-Partek%20Genomics%20Suite%20-%201_1%20\(ANOVAResults\).png?alt=media)

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

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

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-f9be64261d18ddaf18f9998dda6240a8d859e554%2F2017-08-15%2016_55_08-Volcano%20Plot%20Configure_%201_ANOVA-3way.png?alt=media)

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](https://help.partek.illumina.com/partek-genomics-suite/user-manual/visualizations/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.

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-b0707b5d10944e91ce7d472031483bd1c823885f%2F2017-08-15%2016_55_19-Partek%20Genomics%20Suite%20-%201_ANOVA-3way%20\(ANOVAResults\).png?alt=media)

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 (![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-8686f111655525c6027f24eb07460a3a65b27fe2%2Fimage2017-8-29%2013_10_8.png?alt=media))
* Select the **Axes** tab
* Select **Set Cutoff Lines** (Figure 4)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-a19a4d25447492571001f0557c77333e0ee5ff7f%2F2017-08-15%2016_55_32-Plot%20Rendering%20Properties.png?alt=media)

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)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-e261f9fea1dd8cb9222cdf546c54aede945462fb%2F2017-08-16%2009_36_43-Set%20Cutoff%20Lines.png?alt=media)

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).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-904f694f3095864441ffa7ac5e8d65411e0743eb%2F2017-08-15%2016_56_06-Partek%20Genomics%20Suite%20-%201_ANOVA-3way%20\(ANOVAResults\).png?alt=media)

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)

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-f8c52ff89346c57b7e862198b0b172978a0f49e1%2F2017-08-15%2017_00_07-Partek%20Genomics%20Suite%20-%201_ANOVA-3way%20\(ANOVAResults\).png?alt=media)

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.