MaGIC Set Comparison Tool

Welcome to the Set Comparison Tool by the Molecular and Genomics Informatics Core (MaGIC).

How to Use This Tool

  1. Go to the Data Input tab and choose an input mode.
  2. Generic lists: upload one wide table where each column is a set.
  3. DE tables: upload one or more DE results tables (or load the demo).
  4. Optionally rename each set using the editable label fields.
  5. For DE tables, map your columns and set significance / fold-change filters.
  6. Switch between Venn Diagram and UpSet Plot on the Set Comparison tab.
  7. Explore the intersection table and download results.

Two Input Modes

Generic Lists
  • One wide table (CSV/TSV); each column is a set.
  • Rows are list items — genes, proteins, GO terms, anything.
  • Empty cells / NAs are ignored; no filtering is applied.
  • Column headers become set labels (editable).
DE Tables
  • One or more differential-expression results tables.
  • Each file is one comparison/contrast (one set).
  • Map gene ID / log2FC / p-value / padj columns.
  • Filter by significance, fold change, and direction.

Venn Diagrams vs UpSet Plots

Venn Diagrams
  • Best for 2 to 5 sets.
  • Shows exact overlap regions as circles.
  • Intuitive for small numbers of comparisons.
  • Becomes cluttered with more than 5 sets.
UpSet Plots
  • Ideal for any number of sets (especially >5).
  • Displays intersections as a matrix with size bars.
  • Clearly shows the largest / most complex intersections.
  • Scales well to dozens of comparisons.

Input Data


Load synthetic demo data with 5 DE comparisons featuring partially overlapping significant gene sets.

Each column becomes a set; its non-empty values are the members. Empty cells and NAs are ignored.

Uploaded Files

Data Preview

Sets (columns)

Data Preview

One color per set. When on, these drive the Venn fills (intersection regions blend their member colors) and the UpSet set-size bars.

Using Per-set Colors (set above) for fills; intersection regions blend their member colors. Turn off Per-set Colors to use a gradient or palette instead.

Set-size bars use Per-set Colors when that option (above) is on; otherwise the intersection bar color.


Download Plot