Gene List Intersection, Union & Difference — Online Venn Set Calculator

After running two differential expression analyses, the first question is usually “how much do these two gene sets overlap?” No software installation needed — just paste your lists.

The tool does three things: deduplicate → normalize (optionally unify case and strip whitespace) → set operations.

Unify your ID namespace before running set operations. This is the most common mistake: one list uses gene Symbols (TP53), the other uses Ensembl IDs (ENSG00000141510) — the intersection will be 0. Even within Symbols, the same gene can appear under different names across annotation versions (aliases, renamed genes), so for formal analyses it is best to map everything to Ensembl IDs or Entrez IDs first.

A large overlap does not imply biological significance. If both sets contain 3,000 genes against a background of 20,000, the expected overlap by chance is roughly 450. To test whether an overlap is statistically significant, run a hypergeometric test — use the Enrichment Significance Test tool on this site, entering the background size, both list lengths, and the overlap count.