Data, information, knowledge and principle: back to metabolism in KEGG

By Minoru Kanehisa, Susumu Goto, Yoko Sato, Masayuki Kawashima, Miho Furumichi, Mao Tanabe. Nucleic Acids Res., 2013

3,127 citations recorded by the source corpus.

In the hierarchy of data, information and knowledge, computational methods play a major role in the initial processing of data to extract information, but they alone become less effective to compile knowledge from information. The Kyoto Encyclopedia of Genes and Genomes (KEGG) resource (http://www.kegg.jp/ or http://www.genome.jp/kegg/) has been developed as a reference knowledge base to assist this latter process. In particular, the KEGG pathway maps are widely used for biological interpretation of genome sequences and other high-throughput data. The link from genomes to pathways is made through the KEGG Orthology system, a collection of manually defined ortholog groups identified by K numbers. To better automate this interpretation process the KEGG modules defined by Boolean expressions of K numbers have been expanded and improved. Once genes in a genome are annotated with K numbers, the KEGG modules can be computationally evaluated revealing metabolic capacities and other phenotypic features. The reaction modules, which represent chemical units of reactions, have been used to analyze design principles of metabolic networks and also to improve the definition of K numbers and associated annotations. For translational bioinformatics, the KEGG MEDICUS resource has been developed by integrating drug labels (package inserts) used in society.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ceaa55fc43e0db971a49ecf6207f5f1356bd8e70

How researchers see this paper

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

In Molecular Biology

Citations in the corpus

Data Fusion by Matrix Factorization (2013, methodology): “publications from the PubMed database (PMID) (type 4), Medical Subject Headings (MeSH) descriptors (type 5), and KEGG pathways [60] (type 6).”
STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data (2015, background): “A large part of the known interactions comes from manually curated datasets such as DrugBank (19), GPCR-ligand database (GLIDA) (20), Matador (21), the Therapeutic Targets Database (TTD) (22) and the Comparative Toxicogenomics Database (CTD) (23), and several pathway databases including the Kyoto En”
Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics (2016, methodology): “Genes are commonly assigned to pathways using wellestablished databases (such as Gene Ontology[6], KEGG[7], PANTHER[8], REACTOME[9], BIOCARTA[10]) or in-house annotation (based on co-expression[4], for example).”
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm (2014, background): “html) available on the KEGG2 website [38] to identify the associated pathways.”
The BioGRID interaction database: 2015 update (2014, methodology): “…is also involved in renal function and homeostasis (67) Core genes involved in the AAP, as well as AAP-related genes and genes involved in blood pressure (BP) regulation, were identified using curated pathway resources such as KEGG (68) and Reactome (69), as well as Gene Ontology (63) annotations.”
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics (2016, background): “The final result is an annotated table of gene counts per sample that can be linked to the Kyoto encyclopedia of genes and genomes (KEGG) orthology (KO) accession numbers (Kanehisa et al., 2004) or to any other orthologous protein family catalog.”
Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma (2016, methodology): “In addition to HLA, genes participating in the APM pathway were annotated based on the Kyoto Encyclopedia of Genes and Genomes’ (Kanehisa et al., 2014) ‘‘Antigen Processing and Presentation Pathway.”
HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks (2016, methodology): “We add expert-curated PPI directionality and effect information from KEGG (31).”
A Phage Tail-Derived Element with Wide Distribution among Both Prokaryotic Domains: A Comparative Genomic and Phylogenetic Study (2014, neutral): “Key words: bacterial protein translocation, PLTS, T6SS, PVC, Afp, phage tail-like element.”
g:Profiler—a web server for functional interpretation of gene lists (2016 update) (2016, neutral): “Databases such as Reactome (3) and KEGG (4) maintain well-curated collections of known molecular pathways.”
Probiotics, gut microbiota, and their influence on host health and disease (2017, methodology): “Bowtie2 tool [111] enables read alignment to the human genome (reference) and to the KEGG database [112].”
DIANA-miRPath v3.0: deciphering microRNA function with experimental support (2015, background): “The details pane [15] offers information for each miRNA, individual targets and p-values [16].”