Introduction to Pathway Commons

Augustin Luna
26 January, 2016

Research Fellow
Department of Biostatistics and Computational Biology
Dana-Farber Cancer Institute

Topics to be Covered

  • Overview of BioPAX and Pathway Commons
  • Accessing Pathway Commons (PC) using paxtoolsr
    • Searching PC
    • Visualizing PC Data
    • Overlaying Experimental Data on PC Networks
    • Getting Network Statistics
    • Gene Set Enrichment with PC
    • ID Mapping

What is Pathway Commons?

  • Website:
  • An aggregation of public pathway database information
  • Provides data in multiple formats
    • Biological Pathway Exchange (BioPAX) Format
    • Simple Interaction Format (SIF)
    • Gene sets as Gene Matrix Transposed (GMT) Format
  • Provides infrastructure for searching the aggregated pathway data

Biological Pathway Exchange (BioPAX) Format

  • BioPAX:
  • Community-wide effort to represent biological pathways
    • Pathways are collections of interactions that biologists have found useful to group together for organizational, historic, biophysical or other reasons
  • Types
    • Metabolic pathways
    • Signaling pathways
    • Protein-protein interactions
    • Gene regulatory pathways
  • Advanced tutorial on BioPAX

Pathway Commons Homepage