Learn to use KEGG the Kyoto Encyclopedia of Genes and Genomes, an extensive and widely used resource containing information on genes and pathways in a wide range of species. KEGG curates, integrates, and displays information that enables deep understanding of biological systems. Genes, ligands that interact with genes, pathways in which they participate, descriptive terms that clarify the relationships of all of these aspects come together in this fundamental resource. KEGG is a knowledgebase with application to many areas of biological investigation from basic research, to pharmaceutical discovery, and environmental investigations as well. In this introductory tutorial, you will learn about the foundations and features of KEGG, enabling you to efficiently use one of the foundational resources for systems biology.

You will learn:

  • how to navigate KEGG and to perform effective searches on topics of interest
  • how to set the displays for efficient access to the data of interest to you
  • how to customize the colors of displays to represent your own data
  • how to investigate reference and disease pathways, genes, ligands, drugs, and more


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.

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


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: Pathfinder, for exploring paths through data sets: I didn't expect to do another tip on the paths through experiments or data this week. But there must be something in the water cooler lately, and all of these different tools converged on my part of th...

Video Tip of the Week: PathWhiz for graphical appeal and computational readability : "Pathway diagrams are the road maps of biology." This is how the folks from PathWhiz begin their recent paper. I came across it in the Nucleic Acids Research web server issue which was recently announc...

Video Tip of the Week: PANDA (Pathway AND Annotation) Explorer for lists of genes: This week's Video Tip of the Week demonstrates PANDA, a tool for generating and examining annotations that are available for a list of genes, and evaluating them in the context of pathways. Two great t...

Video Tip of the Week: TargetMine, Data Warehouse for Drug Discovery: Browsing around genomic regions, layering on lots of associated data, and beginning to explore new data types I might come across are things that really fire up my brain. For me, visualization is key t...

Bioinformatics tools extracted from a typical mammalian genome project [supplement]: This is Table 1 that accompanies the full blog post: Bioinformatics tools extracted from a typical mammalian genome project. See the main post for the details and explanation. The table is too long to ...


Recent BioMed Central research articles citing this resource

Mosquera-Rendón Jeanneth et al., Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species Prokaryote microbial genomics. BMC Genomics (2016) doi:10.1186/s12864-016-2364-4

Tao Jin et al., An integrated global chemomics and system biology approach to analyze the mechanisms of the traditional Chinese medicinal preparation Eriobotrya japonica – Fritillaria usuriensis dropping pills for pulmonary diseases Basic research. BMC Complementary and Alternative Medicine (2016) doi:10.1186/s12906-015-0983-y

Azevedo Hátylas et al., Intragraft transcriptional profiling of renal transplant patients with tubular dysfunction reveals mechanisms underlying graft injury and recovery. Human Genomics (2016) doi:10.1186/s40246-015-0059-6

Huang Kai-Yao et al., A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. BMC Systems Biology (2016) doi:10.1186/s12918-015-0244-1

Kučerová Lucie et al., Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster Multicellular invertebrate genomics. BMC Genomics (2016) doi:10.1186/s12864-016-2383-1