Upset — Multi-Contrast Intersections

Header: Upset Plot: Multi-Contrast DEG Intersections

The Upset report shows how differentially expressed genes overlap across many contrasts at once. It is the modern alternative to a Venn diagram when you have more comparisons than a Venn can clearly display.

Reading the Plot

• A bar chart shows the size of every intersection (how many genes fall into each combination of contrasts).
• A dot matrix below the bars indicates which contrasts participate in each intersection.
• Bars are sorted so the largest intersections are easy to spot.

Works for any number of contrasts (2+), and stays readable where Venn diagrams break down.

When to use it

Use Upset when comparing 5 or more contrasts, or any time a Venn diagram would be too cluttered. It answers "which combinations of conditions share DEGs, and how many?" For 2–4 contrasts, Venn is often more intuitive.