New approach for understanding genome variations in KEGG

By Minoru Kanehisa, Yoko Sato, Miho Furumichi, Kanae Morishima, Mao Tanabe. Nucleic Acids Res., 2018

1,595 citations recorded by the source corpus.

Abstract KEGG (Kyoto Encyclopedia of Genes and Genomes; https://www.kegg.jp/ or https://www.genome.jp/kegg/) is a reference knowledge base for biological interpretation of genome sequences and other high-throughput data. It is an integrated database consisting of three generic categories of systems information, genomic information and chemical information, and an additional human-specific category of health information. KEGG pathway maps, BRITE hierarchies and KEGG modules have been developed as generic molecular networks with KEGG Orthology nodes of functional orthologs so that KEGG pathway mapping and other procedures can be applied to any cellular organism. Unfortunately, however, this generic approach was inadequate for knowledge representation in the health information category, where variations of human genomes, especially disease-related variations, had to be considered. Thus, we have introduced a new approach where human gene variants are explicitly incorporated into what we call ‘network variants’ in the recently released KEGG NETWORK database. This allows accumulation of knowledge about disease-related perturbed molecular networks caused not only by gene variants, but also by viruses and other pathogens, environmental factors and drugs. We expect that KEGG NETWORK will become another reference knowledge base for the basic understanding of disease mechanisms and practical use in clinical sequencing and drug development.

Subfields: Genetics, Molecular Biology, Surgery

View Paper: https://www.semanticscholar.org/paper/ca5bb07173efa7cce842099caa58fe65e98ae7f2

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

In Surgery

Minoru Kanehisa

Citations in the corpus

KEGG: integrating viruses and cellular organisms (2020, methodology): “In 2017, we started developing the KEGG NETWORK database (2) as a collection of disease-related network variants, which are experimentally observed perturbed molecular networks.”
Comparative Toxicogenomics Database (CTD): update 2023 (2022, background): “External integration of CTD content with imported annotations from the Gene Ontology (GO) (9), KEGG (10), Reactome (11) and BioGRID (12) produces an additional 13 million inferences.”
The reactome pathway knowledgebase (2019, methodology): “A search (1) on a person’s name returns a list (2) of all events (pathways and reactions) with which that person is associated as author or reviewer.”
Linking metagenomics to aquatic microbial ecology and biogeochemical cycles (2019, background): “These approaches are based on intrinsic genomic characteristics or the distribution and abundance of contigs across metagenome samples (Strous et al. 2012; Kang et al. 2015).”
The MetaCyc database of metabolic pathways and enzymes - a 2019 update (2019, background): “MetaCyc and KEGG (20) are both large metabolic pathway database projects that have been under development for more than two decades.”
Comparative Toxicogenomics Database (CTD): update 2021 (2020, background): “External integration of CTD content with annotations from Gene Ontology (GO) (21), KEGG (22), Reactome (23) and BioGRID (24) produces an additional 12 million inferences.”
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics (2019, background): “These include targets of different classes (7–11), drug-binding domains and targeted sites (12), target expression profiles in patients (13,14), activities of targeted agents (15–17), target-regulators (18–22), target-affiliated pathways (23,24), target–drug interaction networks (25–27), and target–”
Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients (2020, methodology): “To inspect genes in specific GO-term and pathway, the GO and KEGG pathway annotation were downloaded from Gene Ontology Resource (Last updated: 22 February 2020) [28] and KEGG database (Last updated: 14 January 2020) [29], respectively.”
Inferring spatial and signaling relationships between cells from single cell transcriptomic data (2020, methodology): “The genes CycD and Jra are taken from Kegg database [12] (Wnt signaling pathway - Drosophila melanogaster).”
Toward understanding the origin and evolution of cellular organisms (2019, background): “These views are now explicitly implemented as network variants in the KEGG NETWORK database with a new type of KEGG map called network variation map.(10) Efforts are being made to make KEGG more useful for understanding molecular mechanisms of diseases and for supporting drug discovery and developme”