Expression browser plot

A plot with bar charts for one or more selected genes/transcripts can be displayed as shown in figure 33.7.

Image expressionbrowser_plot_samples
Figure 33.7: Expression browser plot with total counts per sample for two genes

The genes/transcripts can be selected from the search box in the top section of the side panel, titled "Genes" in figure 33.7. Or they can be selected in another editor. A useful setup is a split view of the expression browser with the table in one and the plot in another editor as shown in figure 33.8. The genes selected in the table will be shown in the plot. The automatic selection can be disabled by unchecking "Link to selections in other editors".

Image expressionbrowser_plot_split_view
Figure 33.8: Split view of expression browser in table and plot with selections in the table reflected in the plot

The "Expression values" section in the side panel determines what the bars represent: total counts, RPKM, TPM or CPM (TMM-adjusted). See The expression browser for more details on these measurements.

If the samples are associated with metadata, there will be a "Grouping" section in the side panel where it can be selected how to group the samples as shown in figure 33.9. The metadata must be associated prior to the creation of the expression browser.

Image expressionbrowser_plot_groups
Figure 33.9: Expression browser plot where samples are grouped and colored as defined by metadata

If multiple groups are selected, they will be nested with all possible combinations starting from the top as shown in figure 33.10.

Image expressionbrowser_plot_groups_nested
Figure 33.10: Expression browser plot with nested grouping

The bars can also be grouped by metadata whilst being colored by sample as shown in figure 33.11. Or the samples can be collapsed altogether so there is only one bar per group, representing the minimum and maximum values along with an indicator for the average (figure 33.12).

Image expressionbrowser_plot_groups_color_by_sample
Figure 33.11: Expression browser plot where samples are grouped and colored by metadata

Image expressionbrowser_plot_groups_aggregate
Figure 33.12: Expression browser plot where samples are collapsed to one bar per metadata group

If the expression browser was created with statistical comparisons, there will be a "Statistical comparison" section in the side panel. The statistical comparisons are used to indicate pairs of groups where a gene is differentially expressed subject to a certain threshold. See figure 33.13.

When the first metadata column selected under the "Grouping" section of the side panel matches the factor used when creating one or more statistical comparisons, then these statistical comparisons are applicable and will be listed under the "Statistical comparison" section.

Image expression_browser_plot_stat_comp
Figure 33.13: Expression browser plot with indication of differentially expressed groups

The thresholds can be defined by plain, FDR or Bonferroni corrected p-value. Multiple thresholds can be input. Pairs of groups are indicated if they satisfy one or more thresholds. An example with multiple thresholds is shown in figure 33.14.

Image expression_browser_plot_stat_comp_multiple
Figure 33.14: Expression browser plot with multiple statistical comparison thresholds

If multiple threshold are defined for the same metric - e.g., FDR p-value below 0.05 and FDR p-value below 0.01 - then a pair of groups has an indication for just the smallest (most specific) threshold.

See Differential Expression for RNA-Seq for more details on statistical comparisons.