8  Appendix: ITCR Tools and Data Visualization

8.1 UCSC Xena Browser

The UCSC Xena Browser enables researchers to explore, analyze, and visualize cancer genomics datasets – both private datasets and data from large public data resources (e.g., TCGA (The Cancer Genome Atlas) and the GDC (Genomic Data Commons)).

The Xena Browser supports analyses such as statistical tests and visualizations such as

• Kaplan-Meier Curves / survival analyses
• Scatter plots
• Bar graphs
• Visual Spreadsheet view (like a heatmap) – see Figure 2 from Goldman et al. (2020)
  • A visual representation of a grid of data (like what would be stored in a spreadsheet)
  • Each column represents genomic or phenotypic data (e.g., gene expression, mutation calls, methylation probes, subtype classifications or age)
  • Each row represents a single biological/experimental entity (e.g., a bulk tumor sample, a cell line, or a single cell)

Goldman, Mary J., Brian Craft, Mim Hastie, Kristupas Repečka, Fran McDade, Akhil Kamath, Ayan Banerjee, et al. 2020. “Visualizing and Interpreting Cancer Genomics Data via the Xena Platform.” Nature Biotechnology 38 (6): 675–78. https://doi.org/10.1038/s41587-020-0546-8.