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:
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.
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 ...
Video Tip of the Week: Entourage and enRoute from the Caleydo team: Have you dreamed of looking at genomic pathway data, with experimental information aligned with known pathway details, and wandering easily from one pathway node to another as you consider the implicat...
What's The Answer? (color genes in a pathway): BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that ar...
Tip of the Week: Whole Cell Simulation software: My twitter feed exploded over the last few days with conflama around the new publication about the simulation of the biological processes in a cell. Most of the ire was aimed at a fawning NYT piece tha...
Video Tip of the Week: BindingDB for binding affinities: Recently when I was adding videos to our SciVee collection, I noticed that there was a set of new videos about BindingDB. This database has been around for a long time, and I was surprised to realize t...
Recent BioMed Central research articles citing this resource
Araínga Mariluz et al., Opposing regulation of endolysosomal pathways by long-acting nanoformulated antiretroviral therapy and HIV-1 in human macrophages. Retrovirology (2015) doi:10.1186/s12977-014-0133-5
Zhu Haifeng et al., Genome-wide transcriptomic and phylogenetic analyses reveal distinct aluminum-tolerance mechanisms in the aluminum-accumulating species buckwheat ( Fagopyrum tataricum. BMC Plant Biology (2015) doi:10.1186/s12870-014-0395-z
Ke Tao et al., ocsESTdb: a database of oil crop seed EST sequences for comparative analysis and investigation of a global metabolic network and oil accumulation metabolism. BMC Plant Biology (2015) doi:10.1186/s12870-014-0399-8
Spichler Anne et al., Microbiology of diabetic foot infections: from Louis Pasteur to ‘crime scene investigation’. BMC Medicine (2015) doi:10.1186/s12916-014-0232-0
Wang Caihua et al., Predicting target-ligand interactions using protein ligand-binding site and ligand substructures Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Systems Biology The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). BMC Systems Biology (2015) doi:10.1186/1752-0509-9-S1-S2