The KEGG resource for deciphering the genome

By Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Yasushi Okuno, Masahiro Hattori. Nucleic Acids Res., 2004

4,908 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/4667ad4302254f67ef8c831ede8e4cd8d0709715

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Citations in the corpus

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis (2013, background): “of Genes and Genomes (KEGG) PATHWAY Database (33), the Enzyme”
CYGD: the Comprehensive Yeast Genome Database (2004, background): “The order of the reaction steps in the pathway is determined by the annotator and checked against other sources including the KEGG pathways.”
HMDB: the Human Metabolome Database (2007, background): “Metabolites are first identified by literature surveys (PubMed, OMIM, OMMBID, text books), data mining (KEGG, Metlin, BioCyc) or experimental methods.”
A human protein-protein interaction network: a resource for annotating the proteome. (2005, neutral): “Linking Y2H Interactions to Regulatory Pathways A direct comparison between the Y2H network and 22 human regulatory pathways from the Kyoto encyclopedia of genes and genomes—KEGG (Kanehisa et al., 2004)—revealed that the two data sets share 162 proteins involved in different signal transduction proc”
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. (2007, methodology): “To identify such functional and regulatory relationships, the Oncomine analysis pipeline includes a comprehensive ‘‘molecular concepts’’ analysis, which spans diverse types of gene sets, including those derived from Gene Ontology [16], InterPro [17], Biocarta, KEGG [18], HPRD [24], and TRANSFAC [19]”
Comparative Genomics in Eukaryotes (2005, methodology): “From the KEGG database (Kanehisa et al., 2004) we took all metabolic maps with indices smaller than 2000.”
The UCSC Genome Browser Database: update 2006 (2005, background): “The pathway section provides links to KEGG (21), NCI/BioCarta (http://www.”
MPact: the MIPS protein interaction resource on yeast (2005, methodology): “To get a notion of the completeness of our interaction collection, we compared our dataset with signal transduction pathways documented in the KEGG pathway database (28).”
Data integration in the era of omics: current and future challenges (2014, background): “…exploitation in biological research involves not only actual datasets but also previous knowledge (sometimes referred to as Biological Domain Data [29]) which is captured in knowledge databases such as Gene Ontology [36] or the many biological pathway databases such as KEGG [37], or Reactome [38].”
Supervised reconstruction of biological networks with local models (2007, neutral): “Contact: Jean-Philippe.Vert@ensmp.fr”
Genome sequence and analysis of the tuber crop potato (2011, background): “We identified 35 DM-specific genes, 11 of which are supported by similarity to entries in the KEGG databas”
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads (2011, positive): “Predicted protein-coding genes were queried using BLASTP program against the eggNOG database [7] for functional composition analysis, and against the KEGG database [8] for pathway mapping analysis with e-value threshold 1.”
Somatic mutation in single human neurons tracks developmental and transcriptional history (2015, neutral): “of Genes and Genomes (KEGG) pathways (51).”
IMG/M: a data management and analysis system for metagenomes (2007, methodology): “These annotations are based on diverse data sources such as COG (13), Pfam (14) and KEGG (15).”