Learn to use the Reactome resource, a knowledgebase of biological processes with high quality, deeply curated assemblies of information about biological pathways, networks, and their components. Reactome includes information on both biological and chemical entities. With all the detailed reports in Reactome and the links provided to many other database resources, researchers can rapidly access vast amounts of information, all from one convenient site. Users may also overlay their gene lists to pathway maps with the Skypainter tool.

You will learn:

  • how to perform basic searches or browse for high-quality biochemical pathway information in Reactome
  • to use specialized Reactome features including the Pathway Analysis, Species Comparison, and Expression Analysis tools
  • to generate custom queries of the underlying database, using the Reactome Mart interface
  • how to search using the Advanced Search and Small molecule Search interfaces, and to use the PathFinder resource


This tutorial is a part of the tutorial group Interaction resources. You might find the other tutorials in the group interesting:

Pathway Interaction Database: A resource of pathway and network data and displays

MINT: Molecular Interaction Database

Cytoscape: An open-source software platform used for visualization and analysis of molecular interaction and network data

BiologicalNetworks: Analyze and visualize molecular interaction networks

BioSystems: Database of Biological Systems

Reactome Legacy: Older version of the current Reactome knowledgebase of biological processes.

GeneMANIA: GeneMANIA: Fast Gene Function Predictions

GenMAPP: A freely available open source software application for visualizing microarray data in the context of biological pathways.

VisANT: A web-based or downloadable software platform used for visualization and analysis of networks and interaction pathways

InterPro: A comprehensive protein signature resource

IntAct protein interaction database: IntAct is an open source database and analysis resource for protein interaction data

KEGG: KEGG, The Kyoto Encyclopedia of Genes and Genomes


Pathways and Interactions : Tools that are involved with protein interactions and pathway features. Some tools are primarily repositories and some offer analysis options.


Video Tip of the Week: Complex Portal with Super Curators: From the same team that brings us the IntAct database for protein interaction data, the Complex Portal offers insights for additional levels of protein interactions that are organized around a biologic...

Friday SNPpets: This week's SNPpets illustrate that everyone's back in the saddle after the holidays with plenty of chatter. New and updated databases, tools, and other news abound. The financial threat to well known ...

Video Tip of the Week: Plant Reactome at Gramene: Reactome is one of our favorite tools to explore pathways. And they cover a wide range of species, which is helpful for many researchers. But there are times when having a topic-specific tool can be ev...

Video Tip of the Week: New Reactome Pathway Portal 3.0: The Reactome pathway browser has long been a favorite of ours. We've watched it evolve over the years, and continue to appreciate the organization and features that it provides for exploring pathways a...

Friday SNPpets: This week's SNPpets includes updates to existing tools, like Reactome and IMG, the biggest JBrowse display I ever saw, various tidbits from #ASHG15 as word clouds, gene editing, slices through personal...


Recent BioMed Central research articles citing this resource

Croze Myriam et al., A genome-wide scan for genes under balancing selection in Drosophila melanogaster Genome evolution and evolutionary systems biology. BMC Evolutionary Biology (2017) doi:10.1186/s12862-016-0857-z

Kim SungHwan et al., Meta-analytic support vector machine for integrating multiple omics data. BioData Mining (2017) doi:10.1186/s13040-017-0126-8

Xu Cheng-Jian et al., The emerging landscape of dynamic DNA methylation in early childhood Human and rodent genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3452-1

Wu Guixian et al., Cecal MicroRNAome response to Salmonella enterica serovar Enteritidis infection in White Leghorn Layer Non-human and non rodent vertebrate genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3413-8

Joehanes Roby et al., Integrated genome-wide analysis of expression quantitative trait loci aids interpretation of genomic association studies. Genome Biology (2017) doi:10.1186/s13059-016-1142-6