Learn to use the Classic Reactome resource, which is an older version of the current Reactome knowledgebase of biological processes. Reactome provides high quality, deeply curated assemblies of information about biological pathways, networks, and their components. Classic Reactome is no longer being updated and therefore its pathway information may be dated, but researchers are able to use favorite tools such as the starry night pathway map and the Skypainter tool for overlaying their gene lists to pathway maps. Knowing how to use classic Reactome features also benefits investigators when confronted with older installations of Reactome associated with other resources, which may not always be in sync with the latest version of the Reactome site.

You will learn:

  • how to navigate through the biochemical pathway information in Classic Reactome
  • how to find diagrams and details about biological pathways
  • ways to link pathway specific information to the participating molecules
TUTORIAL RELATED CONTENT

TUTORIALS

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: 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

CATEGORIES

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

BLOG POSTS

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...

BIOMED CENTRAL

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