MaGIC RNA-seq Heatmap Tool

Welcome to the RNA-seq Heatmap Tool by the Molecular and Genomics Informatics Core (MaGIC).

How to Use This Tool

  1. Navigate to the Data Input tab. Upload your Expression Matrix and Sample Metadata files, or click 'Load Demo Data' to explore with a built-in example.
  2. Submit your data. Click the Submit button. The Heatmap tab will become visible once data is successfully loaded.
  3. Select genes of interest. On the Heatmap tab, display all genes, enter a custom gene list, or query public gene set databases (GO, KEGG, MSigDB Hallmark).
  4. Customize your heatmap. Use the control panels in the left sidebar to adjust colors, annotations, fonts, clustering, row/column splitting, and legend settings.
  5. Resize and download. Use the Resize panel to fine-tune plot dimensions, then download in your preferred format (PNG, PDF, SVG, TIFF, etc.).

Required Input Data Formats

Expression Matrix
  • File format: CSV or TSV
  • Rows: Genes (one gene per row)
  • Columns: Samples (one sample per column)
  • First column: Gene identifiers (symbols or IDs)
  • All remaining columns: Numeric expression values (e.g., log2 normalized counts, VST, TPM)
Gene,   Sample1, Sample2
BRCA1,  6.5,     7.1
TP53,   8.2,     7.9
Sample Metadata
  • File format: CSV or TSV
  • Rows: Samples (one sample per row)
  • First column: Sample names — must match matrix column names exactly
  • Additional columns: Categorical or numeric metadata variables (e.g., Group, Gender, Tissue)
Sample,  Group,   Gender
Sample1, Control, Male
Sample2, Treated, Female

Input Data

Expression Matrix

Sample Metadata

Use the pre-loaded RNA-seq demo data to explore the tool's features.

Demo dataset: 30 cancer-related genes across 9 samples in 3 treatment groups.

Gene Selection

All other plot options update automatically. Click below to apply a new gene selection.


Download Heatmap