Zhao Jin, Yoko Sato, Masayuki Kawashima, Minoru Kanehisa,
The KEGG database and analysis tools (https://www.kegg.jp) have been developed mostly for understanding genes and genomes of cellular organisms. The KO (KEGG Orthology) dataset, which is a collection of functional ... genome to pathways and other molecular networks, enabling KEGG mapping to uncover hidden features in the genome. Although viruses were part of KEGG for some time, they were not fully integrated in the KEGG analysis tools, because the KO assignment rate is ... computationally generated, covering 90% of viral proteins in KEGG. VOCs can be used, in place of KOs, ...
Tópico(s): RNA and protein synthesis mechanisms
2023 - Wiley | Protein Science
Chao Zhang, Zhongwei Chen, Miming Zhang, Shulei Jia,
The KEGG Orthology (KO) database is a widely used molecular function reference database which can be used to conduct ... of most microorganisms. At present, there are many KEGG tools based on the KO entries for annotating ... efficiently extract and sort the annotation results of KEGG still hinders the subsequent genome analysis. There is ... the gene sequences and species information of the KEGG annotations. Here, we present a supporting tool: KEGG_Extractor for species-specific genes extraction and classification, ...
Tópico(s): Machine Learning in Bioinformatics
2023 - Multidisciplinary Digital Publishing Institute | Genes
Qin Peng, Han Cui, Panxin Li, Shuaitao Wang, Shen Fan, Jie Lu, Meng Sun, Heng Zhang, Shougang Wang, Xiaoyan Su, Huihui Fu, Xiaoli Hu, Jinshui Lin, Yu‐Zhong Zhang, Wei Ding, Weipeng Zhang,
... on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Of the 195,721 ± 47,617 predicted ... mapping and summary, the relative abundance of each KEGG gene was revealed. Considering the taxonomic uniqueness of ... way analysis of variance (ANOVA) to identify enriched KEGG genes in the 0.3-MP-10 biofilms ... groups. We found that 3758 or the 6518 KEGG-annotated genes were significantly changed (adjusted p-value < ... gene numbers (Figure S7). Of these significantly-changed KEGG-annotated genes, the top 40 genes, in terms ...
Tópico(s): Bacterial biofilms and quorum sensing
2023 - Wiley | iMeta
Erik D. Huckvale, Hunter Moseley,
... Background The Kyoto Encyclopedia of Genes and Genomes (KEGG) provides organized genomic, biomolecular, and metabolic information and ... for a wide range of analyses and modeling. KEGG follows the principles of data stewardship to be ... to their database entries via their web-accessible KEGG API. However, the overall FAIRness of KEGG is often limited by the library and software ... given programming language. While R library support for KEGG is fairly strong, Python library support has been ... that provides extensive command line level support for KEGG access and utilization. Results We present kegg_pull, ...
Tópico(s): Bioinformatics and Genomic Networks
2023 - BioMed Central | BMC Bioinformatics
Minoru Kanehisa, Miho Furumichi, Yoko Sato, Masayuki Kawashima, Mari Ishiguro-Watanabe,
Abstract KEGG (https://www.kegg.jp) is a manually curated database resource integrating various biological objects categorized into systems, genomic, chemical and health information. Each object (database entry) is identified by the KEGG identifier (kid), which generally takes the form of ... by appending /entry/kid in the URL. The KEGG pathway map viewer, the Brite hierarchy viewer and the newly released KEGG genome browser can be launched by appending /pathway/ ... Together with an improved annotation procedure for KO (KEGG Orthology) assignment, an increasing number of eukaryotic genomes ...
Tópico(s): Microbial Metabolic Engineering and Bioproduction
2022 - Oxford University Press | Nucleic Acids Research
Minoru Kanehisa, Yoko Sato, Masayuki Kawashima,
... contrast to artificial intelligence and machine learning approaches, KEGG ( https://www.kegg.jp ) has relied on human intelligence to develop “ ... of biological systems, especially in the form of KEGG pathway maps that are manually created by capturing knowledge from published literature. The KEGG models can then be used in biological big ... its genome sequence through the simple procedure of KEGG mapping. Here we present an updated version of KEGG Mapper, a suite of KEGG mapping tools reported previously (Kanehisa and Sato, Protein ...
Tópico(s): Machine Learning in Bioinformatics
2021 - Wiley | Protein Science
Abstract KEGG is a reference knowledge base for biological interpretation of large‐scale molecular datasets, such as genome and ... cell and the organism represented in terms of KEGG molecular networks, including KEGG pathway maps, BRITE hierarchies, and KEGG modules. By the process called KEGG mapping, a set of protein coding genes in the genome, for example, can be converted to KEGG molecular networks enabling interpretation of cellular functions and ... features. Here we report a new version of KEGG Mapper, a suite of KEGG mapping tools available ...
Tópico(s): Glycosylation and Glycoproteins Research
2019 - Wiley | Protein Science
Minoru Kanehisa, Yoko Sato, Miho Furumichi, Kanae Morishima, Mao Tanabe,
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 ... 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 ... we call 'network variants' in the recently released KEGG NETWORK database. This allows accumulation of knowledge about ...
Tópico(s): Pancreatic function and diabetes
2018 - Oxford University Press | Nucleic Acids Research
Rose Bernadette Joachim, Gabriel Altschuler, John N. Hutchinson, Hector R. Wong, Yoshihide Hayashizaki, Lester Kobzik,
... the Pharmacogenomics Knowledgebase (PharmGKB), pathway signatures from Wikipathways, KEGG, Netpath and Reactome, and drug signatures from CTD, ... 0.97 −1.91 1.87E-88 Shigellosis (KEGG) −0.93 0.96 −1.88 2.04E-88 Endocytosis (KEGG) −0.82 0.99 −1.82 1.95E- ... 78 9.11E-66 Pathogenic Escherichia coli infection (KEGG) −0.96 0.82 −1.78 1.51E- ... 71E-91 Metabolism of xenobiotics by cytochrome P450 (KEGG) 0.86 −0.98 1.84 2.55E-70 Drug metabolism—cytochrome P450 (KEGG) 0.84 −0.96 1.81 7.02E-66 Steroid hormone biosynthesis (KEGG) 0.97 −0.81 1.78 2.79E- ...
Tópico(s): Neonatal and fetal brain pathology
2018 - Springer Nature | Molecular Systems Biology
Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima,
KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an encyclopedia of genes and genomes. Assigning functional meanings to genes ... higher levels is the primary objective of the KEGG database project. Molecular-level functions are stored in the KO (KEGG Orthology) database, where each KO is defined as ... interactions, reactions and relations in the forms of KEGG pathway maps, BRITE hierarchies and KEGG modules. In the past the KO database was ... better integration of diseases and drugs with the KEGG molecular networks. KEGG is moving towards becoming a ...
Tópico(s): Biomedical Text Mining and Ontologies
2016 - Oxford University Press | Nucleic Acids Research
... can be used as reference for data interpretation. KEGG ( http://www.kegg.jp/ ) is such a reference knowledge base with ... interaction and reaction networks, which is implemented in KEGG pathway maps, BRITE functional hierarchies, and KEGG modules. The other is to expand knowledge on ... concept of orthologs, which is implemented in the KEGG Orthology (KO) system. Thus, KEGG is a generic resource applicable to all organisms ... first present a brief overview of the entire KEGG resource, and then give an introduction of how ...
Tópico(s): Microbial Natural Products and Biosynthesis
2015 - Springer Science+Business Media | Methods in molecular biology
Minoru Kanehisa, Yoko Sato, Masayuki Kawashima, Miho Furumichi, Mao Tanabe,
KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an integrated database resource for biological interpretation of genome sequences and ... associated with ortholog groups and stored in the KEGG Orthology (KO) database. The KEGG pathway maps, BRITE hierarchies and KEGG modules are developed as networks of KO nodes, ... complete genomes are annotated with KOs in the KEGG GENES database, which can be used as a ... set for KO assignment and subsequent reconstruction of KEGG pathways and other molecular networks. As an annotation ...
Tópico(s): Microbial Metabolic Engineering and Bioproduction
2015 - Oxford University Press | Nucleic Acids Research
Tomer Altman, Michael Travers, Anamika Kothari, Ron Caspi, Peter D. Karp,
Abstract Background The MetaCyc and KEGG projects have developed large metabolic pathway databases that are used for a variety of applications including genome analysis and metabolic engineering. ... content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase ... reactions, and pathways in MetaCyc, and those in KEGG. We devoted significant effort to computational and manual ... we evaluated the accuracy of the correspondences. Results KEGG contains 179 module pathways versus 1,846 base ...
Tópico(s): Enzyme Catalysis and Immobilization
2013 - BioMed Central | BMC Bioinformatics
Stephen R. Johnson, Xinjian Qi, A. Ercüment Çiçek, Gültekin Özsoyoğlu,
Kyoto Encyclopedia of Genes and Genomes (KEGG) is an online and integrated molecular database for several organisms. KEGG has been a highly useful site, helping domain scientists understand, research, ... linking sequenced genomes to higher level systematic functions. KEGG databases are accessible through the web pages of ... Third party systems have been built over the KEGG data to provide extensive functionalities. However, there have ... no attempts towards providing a tablet interface for KEGG data. Recognizing the rise of mobile technologies and ...
Tópico(s): Environmental Monitoring and Data Management
2013 - Springer Nature | Health Information Science and Systems
Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, Andreas Zell,
The KEGG PATHWAY database provides a plethora of pathways for a diversity of organisms. All pathway components are directly linked to other KEGG databases, such as KEGG COMPOUND or KEGG REACTION. Therefore, the pathways can be extended with ... structural modeling approaches. As a drawback, KGML-formatted KEGG pathways are primarily designed for visualization purposes and ... present a precise method for processing and converting KEGG pathways into initial metabolic and signaling models encoded ... Finally, we compare several existing conversion tools for KEGG pathways and show that the conversion from KEGG ...
Tópico(s): Computational Drug Discovery Methods
2013 - Springer Science+Business Media | BMC Systems Biology
Minoru Kanehisa, Susumu Goto, Yoko Sato, Masayuki Kawashima, Miho Furumichi, Mao Tanabe,
... 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 ... from genomes to pathways is made through the KEGG Orthology system, a collection of manually defined ortholog ... numbers. To better automate this interpretation process the KEGG modules defined by Boolean expressions of K numbers ...
Tópico(s): Biomedical Text Mining and Ontologies
2013 - Oxford University Press | Nucleic Acids Research
... of carbohydrate-related databases, and so GLYCOSCIENCES.de, KEGG GLYCAN, and the Consortium for Functional Glycomics databases ... the structure. Open table in a new tab KEGG GLYCAN is a part of the Kyoto Encyclopedia of Genes and Genomes (KEGG) resource developed by Kanehisa Laboratories in Japan. Details regarding each of the data sets available in KEGG GLYCAN are available elsewhere (11Aoki-Kinoshita K.F. ... a brief summary is described in this section. KEGG GLYCAN contains glycan structures extracted from CarbBank and ...
Tópico(s): Genomics and Phylogenetic Studies
2013 - Elsevier BV | Molecular & Cellular Proteomics
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for understanding the functions and utilities ... cellular functions. This unit describes protocols for using KEGG, KEGG PATHWAY, KEGG GENES, KEGG SSDB, KEGG EXPRESSION, and KEGG LIGAND. Protocols are also described for how to ... the full breadth of the functionality provided by KEGG.
Tópico(s): Microbial Metabolic Engineering and Bioproduction
2012 - Wiley | Current Protocols in Bioinformatics
Antigoni Elefsinioti, Ömer Saraç, Anna Hegele, Conrad Plake, Nina C. Hubner, Ina Poser, Mihail Sarov, Anthony A. Hyman, Matthias Mann, Michael Schroeder, Ulrich Stelzl, Andreas Beyer,
... Scholar), and Kyoto Encyclopedia of Genes and Genomes (KEGG) (24Kanehisa M. Goto S. Furumichi M. Tanabe M. Hirakawa M. KEGG for representation and analysis of molecular networks involving ... and binary and complex interactions defined in human KEGG pathways. In addition, we selected high confidence interactions ... genes (FUNSET, 412,587 interactions) was extracted from KEGG pathways. FUNSET is composed of gene pairs that ... consists of random pairs of genes from distinct KEGG pathways that are not known to interact physically. ...
Tópico(s): Computational Drug Discovery Methods
2011 - Elsevier BV | Molecular & Cellular Proteomics
Minoru Kanehisa, Susumu Goto, Yoko Sato, Miho Furumichi, Mikio Tanabe,
Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/ or http://www.kegg.jp/) is a database resource that integrates genomic, chemical and systemic functional information. ... in computable forms; namely, in the forms of KEGG pathway maps, BRITE functional hierarchies and KEGG modules. Continuous efforts have also been made to ... linking genomes to the molecular networks through the KEGG Orthology system. Here we report KEGG Mapper, a collection of tools for KEGG PATHWAY, BRITE and MODULE mapping, enabling integration and ...
Tópico(s): Genomics and Phylogenetic Studies
2011 - Oxford University Press | Nucleic Acids Research
Anna Bauer‐Mehren, Laura I. Furlong, Ferrán Sanz,
... BioPAX_Roadmap.html) Pathway database support Reactome Reactome KEGG KEGG (only BioPAX Level 1) PID PathwayCommons Model database ... databases: Reactome, Kyoto Encyclopedia of Genes and Genomes (KEGG), WikiPathways, Nature Pathway Interaction Database (PID) and Pathway ... available, example client in Java SBML Level 2 KEGG http://www.genome.jp/kegg/pathway.html KGML (default format) SOAP web service ... well as to other pathway databases, such as KEGG (Kanehisa and Goto, 2000) are provided. Pathways are ... be programmatically accessed through a SOAP web service. KEGG KEGG is not only a database for pathways ...
Tópico(s): Gene expression and cancer classification
2009 - Springer Nature | Molecular Systems Biology
Minoru Kanehisa, Michihiro Araki, Susumu Goto, Masahiro Hattori, Mika Hirakawa, Masumi Itoh, Tsutomu Katayama, Shuichi Kawashima, Shujiro Okuda, Toshiaki Tokimatsu, Yoshihiro Yamanishi,
KEGG ( http://www.genome.jp/kegg/ ) is a database of biological systems that integrates genomic, chemical and systemic functional information. KEGG provides a reference knowledge base for linking genomes ... a genomic or transcriptomic content of genes to KEGG reference pathways to infer systemic behaviors of the cell or the organism. In addition, KEGG provides a reference knowledge base for linking genomes ... target relationships, through the process of BRITE mapping. KEGG BRITE is an ontology database representing functional hierarchies ...
Tópico(s): Genetics, Bioinformatics, and Biomedical Research
2007 - Oxford University Press | Nucleic Acids Research
Kiyoko F. Aoki‐Kinoshita, Minoru Kanehisa,
KEGG is a database resource (http://www.genome.jp/kegg/) that provides all knowledge about genomes and their ... as well as their interactions with the environment. KEGG is categorized in terms of building blocks in the genomic space, known as KEGG GENES, the chemical space, KEGG LIGAND, as well as wiring diagrams of interaction and reaction networks, known as KEGG PATHWAY. A fourth database called KEGG BRITE was also recently incorporated to provide computerized annotations and pathway reconstruction based on the current KEGG knowledgebase. KEGG BRITE contains KEGG Orthology (KO), a ...
Tópico(s): Chromosomal and Genetic Variations
2007 - Springer Science+Business Media | Methods in molecular biology
Ruei-Chi Richie Gan, Eugene C. Yi, Yulun Chiu, Hookeun Lee, Yu-chieh P. Kao, Timothy H. Wu, Ruedi Aebersold, David R. Goodlett, Wailap Victor Ng,
... in the Kyoto Encyclopedia of Genes and Genomes (KEGG) 1The abbreviations used are: KEGG, Kyoto Encyclopedia of Genes and Genomes; p, PeptideProphet ... form of a template of interactions from the KEGG database. Cross-reference between pathway maps from KEGG PATHWAYS database and enzyme/gene information from KEGG LIGAND database implemented the integration between proteins and ... The tool set organized the proteomic data and KEGG pathway information in a summary table. Each row ... and HalnoaFactory.java were developed to process the KEGG pathways KEGG mark-up language (KGML) files and ...
Tópico(s): Microbial Community Ecology and Physiology
2006 - Elsevier BV | Molecular & Cellular Proteomics
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for analyzing cells and organisms from ... four databases: PATHWAY, GENES, LIGAND and BRITE. The KEGG PATHWAY database provides pathway diagrams, represented as networks ... according to organism or as generic "reference" maps. KEGG GENES is the collection of genes that are ... in the complete genomes that are registered in KEGG. It serves as the repository of genes linked from the pathway diagrams. KEGG LIGAND is a database of compounds, glycans, reactions ...
Tópico(s): Genomics and Phylogenetic Studies
2006 - Pesticide Science Society of Japan | Nippon Nōyaku Gakkaishi
Kiyoko F. Aoki‐Kinoshita, Minoru Kanehisa,
Abstract KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for understanding the functions and utilities of ... cellular functions. This unit describes protocols for using KEGG, KEGG PATHWAY, KEGG GENES, KEGG SSDB, KEGG EXPRESSION, and KEGG LIGAND. Protocols are also described for how to ... the full breadth of the functionality provided by KEGG.
Tópico(s): Glycosylation and Glycoproteins Research
2005 - Wiley | Current Protocols in Bioinformatics
... for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for linking genomes ... categorized as building blocks in the genomic space (KEGG GENES) and the chemical space (KEGG LIGAND), and wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY). A fourth component, KEGG BRITE, has been formally added to the KEGG suite of databases. This reflects our attempt to ... the new chemical genomics initiatives, the scope of KEGG LIGAND has been significantly expanded to cover both ...
Tópico(s): Enzyme Catalysis and Immobilization
2005 - Oxford University Press | Nucleic Acids Research
Shuichi Kawashima, Toshiaki Katayama, Yoko Sato, Minoru Kanehisa,
We have been making the KEGG system available at GenomeNet [2]. KEGG is a suite of databases including GENES, SSDB, PATHWAY, LIGAND, LinkDB, etc. for genome research ... troublesome for the researchers who want to use KEGG in an automated manner. Besides, from the database ... have started developing a new web service called KEGG API [5]. Using KEGG API, the user can access to all the resources stored in KEGG as a batch processing style without any limitations ... also means that the user can embed the KEGG system into in-house programs to analyze his/ ...
Tópico(s): Biomedical Text Mining and Ontologies
2003 - Imperial College Press | Proceedings Genome Informatics Workshop/Genome informatics
Minoru Kanehisa, Miho Furumichi, Yoko Sato, Mari Ishiguro-Watanabe, Mao Tanabe,
KEGG (https://www.kegg.jp/) is a manually curated resource integrating eighteen databases categorized into systems, genomic, chemical and health information. It also provides KEGG mapping tools, which enable understanding of cellular and ... functions from genome sequences and other molecular datasets. KEGG mapping is a predictive method of reconstructing molecular ... of functional orthologs. Since the introduction of the KEGG NETWORK database, various diseases have been associated with ... inhibit or activate specific cellular signaling pathways. The KEGG pathway maps are now integrated with network variation ...
Tópico(s): CRISPR and Genetic Engineering
2020 - Oxford University Press | Nucleic Acids Research
Oshrat Raz, Galit Granot, Metsada Pasmanik‐Chor, Pia Raanani, Uri Rozovski,
... GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to predict target gene ... miR only. (B) GOTERM BP (upper panel) and KEGG pathway (lower panel) enrichment analysis for all circ_ ... signaling pathway related, p ≤ 4 × 10–5, DAVID, KEGG), pink (E, MAPK cascade related, p ≤ 0.02, ... cancer related, p ≤ 9.3 × 10–21, WEBGESTALT, KEGG) rectangles. The potentially targeted mRNAs are displayed in ... GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to predict target gene ...
Tópico(s): Galectins and Cancer Biology
2020 - Elsevier BV | Experimental Hematology