Free AI-Assisted

Gene List Overlap Calculator

Compare 2–8 gene lists with UpSet plots, Venn diagrams, alias normalization, and hypergeometric p-values—no upload. Built-in AI agent assistant support.

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Key facts

Key facts about Gene List Overlap Calculator
FactValue
Inputs2–8 named lists; newlines, commas, tabs, semicolons, or spaces
SpeciesHuman, Mouse, Rat, Yeast, Zebrafish (NCBI Gene synonyms)
Alias normalizationOptional; maps synonyms to canonical gene symbols
StatisticsHypergeometric p-values and Representation Factors (configurable N, default 20,000)
VisualizationsUpSet plot matrix (2–8 lists) or classic Venn diagram (2–4 lists)
Item limitsUp to 5,000 items per list (client-side deduplication)
ExportSVG vector, PNG raster, per-group CSV, all-groups CSV
Enrichr integrationOne-click pathway enrichment from subset detail drawer
Runs in browserYes — calculations run locally; lists stay private
Account requiredNo

What it does

Comparing gene lists manually across experimental conditions or databases causes errors from mismatched aliases and unscalable Venn diagrams. The Gene List Overlap Calculator computes exact intersections, exclusive sets, and pairwise statistical significance across 2 to 8 lists in your browser—without writing R scripts or uploading data.

Paste items separated by newlines, commas, tabs, or semicolons into up to 8 named list cards. Toggle optional Gene symbol normalization to map aliases (such as p53 to TP53) across Human, Mouse, Rat, Yeast, or Zebrafish using static NCBI Gene synonym tables. Set your background universe size (default 20,000 genes) for hypergeometric significance testing and representation factor scoring.

Results display as an interactive UpSet plot matrix (default for 2–8 lists) or classic Venn diagram (for 2–4 lists), paired with a sortable intersection table and a pairwise p-value summary card. Click any overlap subset to inspect item lists in a detail drawer, copy plain text, download CSV files, export SVG/PNG figures for publication, or launch direct pathway enrichment in Enrichr.

Why researchers use it

  • Compare up to 8 gene lists without writing R code
  • Map gene symbol aliases to canonical NCBI symbols
  • Calculate hypergeometric overlap p-values and fold enrichment
  • Export publication-ready SVG and PNG figures instantly
  • Send intersection subsets directly to Enrichr for pathway analysis
  • Keep proprietary genomic data private in local browser storage

Best for

  • Differential gene expression (RNA-seq / microarray) set comparison
  • ChIP-seq and ATAC-seq peak target gene list intersections
  • Cross-species ortholog list comparison after alias mapping
  • Multi-omics gene hit integration across 2 to 8 experimental groups
  • Generating publication-grade UpSet plots and Venn diagrams

When to use this vs alternatives

Choose the Gene List Overlap Calculator when comparing 2 to 8 gene sets requiring alias normalization, hypergeometric p-values, or SVG figures. Use DNA RevComp & Primer Toolkit for sequence manipulation or Sequence Property Calculator for molecular weight and GC% calculations. Venny or InteractiVenn suit simple 2- to 3-list comparisons when alias normalization and statistical p-values are unnecessary.

What makes it different

Standard Venn tools like Venny and InteractiVenn become unreadable past 3 or 4 sets and cannot reconcile gene symbol aliases like p53 versus TP53. Writing custom R code with UpSetR or ComplexUpset provides scalable plots but requires programming skills, manual data formatting, and separate downstream GO pathway tools.

This browser tool combines multi-list comparison for 2 to 8 sets, species-aware NCBI alias normalization, hypergeometric p-values, UpSet and Venn visualizations, SVG/PNG export, and one-click Enrichr pathway integration in a zero-setup workspace. Researchers switch when traditional Venn diagrams obscure multi-set overlaps or when alias mismatches create false negative non-overlaps.

How to get started

  1. Open the workspace and stay on the Input tab.
  2. Paste gene or item lists into at least two list cards (or click Load example for a 3-list demo).
  3. Select species and toggle Gene symbol normalization if input lists contain alias symbols.
  4. Set background universe size (default 20,000) and click Compare lists.
  5. Review the UpSet plot or Venn diagram on the Results tab, alongside the pairwise statistical card.
  6. Click any intersection row to open the detail drawer to copy items, download CSV, or launch Analyze in Enrichr.

Frequently asked questions

How do I calculate gene list overlap statistics?
Enter two or more gene lists and set a background universe size (default 20,000 genes). The tool computes set intersections and tests pairwise significance using the hypergeometric distribution. It reports the overlap count, expected overlap by chance, representation factor (fold enrichment), and p-value.
How does gene symbol alias normalization work?
When enabled, the tool compares each input item against static NCBI Gene synonym maps for Human, Mouse, Rat, Yeast, or Zebrafish. Aliases like p53 map to canonical symbols (TP53) before set operations occur. Unmatched tokens remain as entered and are flagged in the detail drawer.
Why should I use an UpSet plot instead of a Venn diagram?
Venn diagrams become visually cluttered and mathematically inaccurate beyond 3 or 4 sets. UpSet plots represent intersections using a matrix grid and bar chart, cleanly showing all 2ⁿ−1 subset combinations for up to 8 lists without visual overlap distortion.
Can I perform pathway enrichment directly on overlap gene sets?
Yes. Clicking any intersection row in the results table opens a detail drawer listing all genes in that subset. Click Analyze in Enrichr to transmit the gene list directly to Enrichr for GO, KEGG, and Reactome pathway enrichment analysis.
Are my gene lists uploaded to a remote server?
No. List parsing, deduplication, alias mapping, set intersections, and chart rendering execute entirely inside your local browser. Your data remains private on your machine unless you explicitly choose to launch external Enrichr analysis.
Can I use an AI agent with the Gene List Overlap Calculator?
Yes. The workspace features an in-browser AI assistant that helps format gene lists, validate inputs, and interpret hypergeometric p-values. External AI agents can also interact with the calculator via MCP using pepkio_smart-list-overlap.

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Last updated . Pepkio builds free lab calculators alongside bioinformatics CRO services.