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Pathways (PWs) are molecular workflows converting chemical entities (metabolic PWs) or transducing a signal (signalling PWs) in a living cell or fluid. More generally, a pathway is the graphical representation of all kinds of relationships between entities/genes/proteins/chemicals that build a biological workflow and explain a cellular or molecular set of functions. Other types of pathway belong to the fields of genetics and neurobiology but fall out of the simplified scope of this page.

Pathway editing tools

  • Ingenuity pathway Analysis (commercial product, VIB users only)
  • Cytoscape - a universal pathway and network editing tool with many valuable plugins
  • PathVisio
  • PathwayTools - the official programmatic front end to BioCyc (free for academia)
  • Bioconductor includes packages for the analysis and editing of Pathway data for the 'geeks' among us.

Pathway databases

  • KEGG Pathway - the canonical collection of manually curated pathway maps (limited access since 2009)
  • BioCyc is a collection of 3530 Pathway/Genome Databases (PGDBs), with tools for understanding their data. It should be replacing KEGG sooner or later and supports many more species. As examples; EcoCyc, AraCyc and HumanCyc are part of BioCyc.
  • Reactome is a curated and peer reviewed pathway database with online accompanying tools. There is also a Reactome plugins for Cytoscape and a package in Bioconductor.
  • NetPath - a curated resource of signal transduction pathways in humans.

Organism Dedicated genome databases

A non-exhausting list is provided at Wikipedia

Pathway analysis tools (only non-commercial ones)

  • MapMan is a user-driven tool that displays large datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other processes. This tools is for Plant only (for once ;- ).