Output of the Differential Expression tools

Differential expression tools output one or more statistical comparison tracks or tables.

It can often be useful to collect all samples in an expression browser (Create Expression Browser), and visualize it alongside the statistical comparison, see Arrange views in View Area.

Statistical comparisons have a number of views (figures 33.78 and 33.79), displaying information about the performed test in different formats:

Using tracks differential expression results can be stacked with data of different types based on a compatible genome, and linked viewed opened. See Track lists. See also Working with tracks for details about working with individual tracks.

Note that the track view is not available for statistical comparison tables.

Image statistical_comparison_track
Figure 33.78: Views of a statistical comparison. Top: Track view. Bottom: Table view. The views are linked: selecting a feature in one view, also selects the feature in the other view.

The statistical comparison table offers, for each feature, the following

At the bottom of the table view, the following buttons are available:

Volcano plots

The volcano plot (figure 33.79) shows the relationship between the fold changes and p-values. The log2 fold changes and -log10 p-values are plotted on the x- and y-axis, respectively. Features of interest are typically those with large fold changes (far from $ x=0$) that are statistically significant, i.e. have small p-values (far from $ y=0$). They are located in the upper left (down-regulated) and upper right (up-regulated) hand corners of the volcano plot.

Image stat_comp_volcano
Figure 33.79: Customized volcano plot. Features are colored using gradients and those with low fold changes or high p-values are faded. The legend is shown in the upper right corner. The plot uses transparency for better visualization of overlapping points. Features in the bottom left corner are selected to highlight a "wing" pattern. The horizontal axis range is adjusted to center the plot.

Volcano plots can exhibit unexpected patterns looking like "wings", such as the one in orange in the bottom left corner in figure 33.79. These patterns reflect the mathematical relationship between fold changes and p-values, which can be exposed when there are few replicates and expression is low in one condition. For example, expression counts for two genes might be (5,5) vs (0,0) and (5,6) vs (0,1). These two genes would appear in the same "wing". Two other genes with expression counts (5,5) vs (0,1) and (5,6) vs (0,1) would be in another "wing".

The following can be configured in the Side Panel:

Volcano plot. General options for configuring the content and coloring.

Annotations. Options for coloring features using annotations (figure 33.80).

Image volcano_by_annotation
Figure 33.80: The Annotations group in the Side Panel. All biotype annotations containing "r" are shown, and protein coding features are colored using turquoise.

Thresholds. Options for fading features with small fold changes or non-significant p-values.

Selected points. Options for configuring selections.

Points in the volcano plot can be selected by

Hold down the Ctrl key (Image command_key_web on Mac) to perform an additional selection.

Dot properties.

Axis ranges. Options for configuring the the ranges of the two axes.

Note: When the potential number of labels is high, only a subset is shown. Zooming in and out may affect the labels shown.

The plot right-click menu offers the following options, for both Colored points and Selected points: