PathScore: a web tool for identifying altered pathways in cancer data

Bioinformatics. 2016 Dec 1;32(23):3688-3690. doi: 10.1093/bioinformatics/btw512. Epub 2016 Aug 8.

Abstract

PathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects.

Availability and implementation: Web application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at: github.com/sggaffney/pathscore with a GPLv3 license.

Contact: stephen.gaffney@yale.edu.

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • Humans
  • Internet*
  • Metabolic Networks and Pathways / genetics
  • Mutation
  • Neoplasms / genetics*
  • Software*