List of tools to visualize multidimensional cancer genomics data

About source of this article

This is a blog written by the members of the Biomedical Genomics group at the University Pompeu Fabra in Barcelona. With this blog we want to have a flexible means to communicate with the research community and the users of tools and resources developed in our lab (e.g. IntOGenGitools) Read more

Please note that the portals and tools listed in the table below were selected because they allow to visualize several dimensions of cancer genomics data together. The list thus does not pretend to be a comprehensive set of resources for cancer research. Multiple dimensions in cancer genomics data are different variables measured per tumor sample and genomic elements (for example, the genes), such as copy number alterations (CNAs), mutations, gene expression changes and methylation changes.

Updates from the publication of the review:
We have recently learnt about two new interesting tools for multidimensional cancer genomics data visualization that are now included in the updated table in this post.

Cancer Landscapes, which uses network visualization to represent associations between variables (such as mRNA expression, methylation or copy number alterations). The associations are computed using high performance optimization methods.

Next Generation Clustered Heatmaps, which uses matrix heatmaps to visualize genomic and transcriptomic data from tumors. The tool allows to zoom in and out, and pan across the heatmap to see details at many levels of resolution. Other interactive controls enable searching for specific heatmap entries, generating production quality PDFs, and linking out to information related to rows, columns, and individual heatmap entries. Data from TCGA is ready to be explored with this tool.

Another update we would like to mention is the brand new version of Gitools, (v.2.0), which is available as a preview version. This new version contains substantial changes, among which we would like to highlight that, 1) it is now able to load very large data matrices in a memory efficient way; 2) it possesses an improved user’s interface; and 3) it includes new functions specifically designed for the study of multidimensional cancer genomics data.

 Table of tools listed in alphabetical order
We distinguish between three main approaches commonly used to represent multidimensional oncogenomics data: genomic coordinates, heatmaps and networks. The tools in the table are classified according to the visualization type they use.

NameVisualization typeTool type
cBio Cancer Genomics PortalNetworks – Matrix HeatmapsWebtool
Cancer Landscapes NetworksWebtool
CircleMap Circular HeatmapsCommand line application – Webtool
Circos Circular Genomic CoordinatesCommand Line Application
Caleydo StratomeX Matrix Heatmap with option to visualize pathway mapsDesktop Application (Java)
Cancer LandscapesNetworksWebtool
Cytoscape NetworksDesktop Application (Java)
GenomicaMatrix Heatmap – Genomic coordinatesDesktop Application (Java)
Gitools Matrix Heatmap with interactive featuresDesktop Application (Java)
Integrative Genomics Viewer (IGV) Genomic CoordinatesDesktop Application (Java)
IntOGen Matrix Heatmaps with interactive featuresWebtool
NAViGaTOR NetworksDesktop Application (Java)
Next Generation Clustered HeatmapsHeatmapsWebtool
Regulome Explorer Circular and linear Genomic coordinates – NetworksWebtool
Savant Genome Browser Genomic CoordinatesDesktop Application (Java)
The Cancer Genome Workbench Genomic Coordinates –HeatmapWebtool
UCSC Cancer Genomics Browser Genomic Coordinates –HeatmapsWebtool