MaGIC Set Comparison Tool

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

How to Use This Tool

  1. Navigate to the Data Input tab.
  2. Upload two or more DESeq2 results tables (CSV/TSV) or load the demo data.
  3. Optionally rename each comparison using the editable label field.
  4. Map your columns (gene ID, log2FoldChange, padj) and click Submit .
  5. Adjust significance and fold-change filters on the Set Comparison tab.
  6. Switch between Venn Diagram and UpSet Plot views.
  7. Explore the intersection table and download results.

Venn Diagrams vs UpSet Plots

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

Required Input Data

This tool accepts one or more DESeq2 results tables in CSV or TSV format. Each file represents one comparison/contrast and should contain at minimum:

  • Gene identifier column (e.g., gene symbol or Ensembl ID).
  • log2FoldChange — the log2 fold change from differential expression analysis.
  • pvalue — the raw p-value.
  • padj — the adjusted p-value (Benjamini-Hochberg or similar).

Each uploaded file will be treated as one set. Files are labeled by their filename by default, but you can provide custom labels on the Data Input tab.

Input Data

Load synthetic demo data with 5 DESeq2 comparisons featuring partially overlapping significant gene sets.

Uploaded Files

Data Preview


Download Plot