Create Pathway Heatmaps

Upload your logCPM data and generate interactive heatmaps

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Try HeatPath with Demo Data

Load example RNA-seq data instantly

Normalized Count Matrix (logCPM)
Sample Metadata
Select Database
Select Pathway(s)
Plot Title (optional)

Preview Your Data



Heatmap Output

What is HeatPath?

HeatPath allows users to generate heatmaps of gene expression for selected pathways using RNA-seq data. It supports GO, KEGG, and Reactome gene sets, and provides interactive plotting and annotation options.

Usage Instructions

  1. Upload logCPM expression matrix with gene symbols or Ensembl IDs.
  2. Upload sample information CSV with 'sample_name' and 'group' columns.
  3. Select a pathway database and choose one or more pathways.
  4. Optionally add a title for each plot and generate plots interactively.
  5. Use download buttons to save matrix data and remove buttons to clean up plots.

What data are plotted?

  1. For each selected pathway, the app extracts the corresponding genes from your expression matrix and generates a heatmap.
  2. To make the heatmaps easier to interpret, the expression values are standardized within each gene: this means converting the logCPM values into Z-scores by subtracting the mean and dividing by the standard deviation across samples.
  3. Red indicates higher-than-average expression for that gene in a sample, while blue indicates lower-than-average expression. White indicates expression close to the gene's average.