Pathways Heatmap

Gene Set Enrichment Analysis

General Description

Our Gene Set Enrichment Pathways tool aims to provide a standard ssGSEA enrichment score for each of our PDX models.

Pathways Heatmap Input

Pathways Heatmap Input

Pathways Heatmap Input

  1. Pathways. Select your pathway of interest.
  2. Cancer Type. Select cancer type of interest from the dropdown menu or leave blank for all cancer types.
  3. Model/Sample. Select specific models with available data or leave blank for all available models with data.
  4. View.
  5. Export. Analysis can be exported as a PNG image.
  6. Visualize. Data inputs can be populated and visualized in Oncoprint, Mutation Mapper, and High/Low Expression.
  7. Loading Task Bar. Building your requested visualization may take some time. The status of your request will be displayed here.

Pathways Heatmap Visualization

Pathways Heatmap Visualization

Pathways Heatmap Visualization

  1. Filter. When multiple pathways are selected you can filter which are visible.
  2. Color Settings. Change the heatmap data colors.
  3. Dendrogram. Shows each model with data for a chosen pathway and the z-score for each of the models.
  4. Zoom. After selecting a row you can click the ‘Zoom’ Icon to have a closer look at the models within that row.

The Z-score values shown provide a standardized metric of a specified gene set enrichment score across all of the samples in our database. A higher Z-score value shown for a specified model would represent higher than “average” expression of the gene set within that model when compared to all models in our database. For example, a sample with a Z-score of 2 indicates this sample has a score 2 standard deviation higher than the average score in the database.

Key Terms

ssGSEA - Single Sample Gene Set Enrichment Analysis

Common Analysis with Pathways Heatmap

Coming Soon!!

References and Acknowledgements