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PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data.

Istemi Bahceci1, Ugur Dogrusoz1, Konnor C La2

  • 1Department of Computer Engineering, Bilkent University, Ankara, Turkey.

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PathwayMapper is a new web tool for visualizing and editing cancer pathways. It allows biologists to overlay genomic alteration data and collaborate on pathway construction, simplifying cancer genomics data exploration.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Cancer Genomics

Background:

  • Existing network visualization tools are complex for biologists.
  • Biologists prefer simplified, curated pathway diagrams for cancer genomics data.
  • The Cancer Genome Atlas (TCGA) pathway diagrams are a common preference.

Purpose of the Study:

  • To develop a user-friendly web-based tool for cancer pathway visualization and editing.
  • To enable overlaying of genomic alteration data from cBioPortal onto pathways.
  • To facilitate collaborative pathway construction among scientists.

Main Methods:

  • Developed PathwayMapper, a web-based tool accessible via common web browsers.
  • Implemented functionality for viewing pre-curated cancer pathways.
  • Integrated a graphical editor for creating new pathways.
  • Added collaborative mode with support for concurrent modifications and conflict resolution.

Main Results:

  • PathwayMapper provides a simplified interface for exploring cancer genomics data.
  • Users can overlay genomic alteration data from cBioPortal onto curated or custom pathways.
  • Collaborative mode allows interactive, concurrent pathway construction with conflict resolution.

Conclusions:

  • PathwayMapper addresses the need for simplified cancer pathway visualization and editing.
  • The tool enhances the exploration of cancer genomics data for biologists.
  • Collaborative features promote efficient pathway construction and data sharing.