Volcano — Differential Expression Analysis

Header: Volcano Plot: Differential Expression Analysis

The Volcano plot is the primary visualization for differential expression results. It plots every gene as a point, with the x-axis showing the log2 Fold Change (magnitude of expression difference) and the y-axis showing the -log10 Adjusted p-value (statistical significance).

Reading the Plot

• Upregulated genes (red dots) appear on the right side of the plot — they have a positive fold change and pass both the p-value and fold change thresholds.
• Downregulated genes (blue dots) appear on the left side — they have a negative fold change and pass both thresholds.
• Non-significant genes (grey dots) cluster near the center and bottom of the plot.

The plot title includes the total number of significant genes (e.g., "Significant: 2526"). Annotation labels on the plot show the count of downregulated genes (e.g., "n=618") on the left and upregulated genes (e.g., "n=1908") on the right.

Threshold Lines

Dashed vertical lines mark the log2 Fold Change thresholds (positive and negative), and a horizontal dashed line marks the adjusted p-value threshold. You can adjust these in the sidebar Filters section. The style and color of these lines can be changed using the Threshold Lines controls in the Appearance section.

Genes — All (Expandable Table)

Below the Volcano plot, an expandable section labeled "Genes — All" provides the full gene-level data table with all expression statistics.