While the network visualization module in cBioPortal is a powerful exploration tool, most biologists are more comfortable with the kind of simplified, curated pathway diagrams that are featured in many manuscripts from The Cancer Genome Atlas (TCGA) . With the motivation of creating a platform that provides more intuitive pathway diagrams, yet supports these with rich data ‘decoration’ and analysis with access to data in cBioPortal, with attractive visualization, a tool named PathwayMapper based on Cytoscape.js was developed. PathwayMapper is a valuable tool for constructing pathways from scratch. One can also use it as a viewer to overlay cancer genomics data on existing "template" pathways like those that appeared in TCGA papers. Ultimately, this project has two main purposes. First one is improving PathwayMapper with new attaractive features for both local and colloborative modes. Second one is integrating PathwayMapper into cBioPortal as an alternative to the cBioPortal's current network view.


Kaan Sancak


  • Ugur Dogrusoz
  • Onur
  • JJ Gao