515:. The KEGG pathway maps are drawn based on experimental evidence in specific organisms but they are designed to be applicable to other organisms as well, because different organisms, such as human and mouse, often share identical pathways consisting of functionally identical genes, called orthologous genes or orthologs. All the genes in the KEGG GENES database are being grouped into such orthologs in the KEGG ORTHOLOGY (KO) database. Because the nodes (gene products) of KEGG pathway maps, as well as KEGG modules and BRITE hierarchies, are given KO identifiers, the correspondences are established once genes in the genome are annotated with KO identifiers by the
1835:
27:
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environmental samples in metagenomics studies. In contrast, KEGG modules in the KEGG MODULE database are higher-resolution, localized wiring diagrams, representing tighter functional units within a pathway map, such as subpathways conserved among specific organism groups and molecular complexes. KEGG modules are defined as characteristic gene sets that can be linked to specific metabolic capacities and other
1847:
569:
biological systems. However, disease pathway maps cannot be drawn for most diseases because molecular mechanisms are not well understood. An alternative approach is taken in the KEGG DISEASE database, which simply catalogs known genetic factors and environmental factors of diseases. These catalogs may eventually lead to more complete wiring diagrams of diseases.
556:
reactions, and KEGG ENZYME for reactions in the enzyme nomenclature. Currently, there are additional databases: KEGG GLYCAN for glycans and two auxiliary reaction databases called RPAIR (reactant pair alignments) and RCLASS (reaction class). KEGG COMPOUND has also been expanded to contain various compounds such as
555:
The databases in the chemical information category, which are collectively called KEGG LIGAND, are organized by capturing knowledge of the chemical network. In the beginning of the KEGG project, KEGG LIGAND consisted of three databases: KEGG COMPOUND for chemical compounds, KEGG REACTION for chemical
483:
database containing hierarchical classifications of various entities including genes, proteins, organisms, diseases, drugs, and chemical compounds. While KEGG PATHWAY is limited to molecular interactions and reactions of these entities, KEGG BRITE incorporates many different types of relationships.
389:
The KEGG PATHWAY database, the wiring diagram database, is the core of the KEGG resource. It is a collection of pathway maps integrating many entities including genes, proteins, RNAs, chemical compounds, glycans, and chemical reactions, as well as disease genes and drug targets, which are stored as
471:
The metabolism section contains aesthetically drawn global maps showing an overall picture of metabolism, in addition to regular metabolic pathway maps. The low-resolution global maps can be used, for example, to compare metabolic capacities of different organisms in genomics studies and different
568:
In KEGG, diseases are viewed as perturbed states of the biological system caused by perturbants of genetic factors and environmental factors, and drugs are viewed as different types of perturbants. The KEGG PATHWAY database includes not only the normal states but also the perturbed states of the
605:
In July 2011 KEGG introduced a subscription model for FTP download due to a significant cutback of government funding. KEGG continues to be freely available through its website, but the subscription model has raised discussions about sustainability of bioinformatics databases.
504:. The KEGG GENES database contains gene/protein-level information and the KEGG GENOME database contains organism-level information for these genomes. The KEGG GENES database consists of gene sets for the complete genomes, and genes in each set are given
539:
are transformed by these reactions. A set of enzyme genes in the genome will identify enzyme relation networks when superimposed on the KEGG pathway maps, which in turn characterize chemical structure transformation networks allowing interpretation of
264:) in the pathway. This has enabled the analysis called KEGG pathway mapping, whereby the gene content in the genome is compared with the KEGG PATHWAY database to examine which pathways and associated functions are likely to be encoded in the genome.
1690:
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and other health-related substances, which are outside the category of approved drugs, are stored in the KEGG ENVIRON database. The databases in the health information category are collectively called KEGG MEDICUS, which also includes
275:
and reactions, and wiring diagrams of molecular interaction and reaction networks. This concept is realized in the following databases of KEGG, which are categorized into systems, genomic, chemical, and health information.
847:
Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. (1995). "Whole-genome random sequencing and assembly of
Haemophilus influenzae Rd".
588:, and other molecular interaction network information in the KEGG pathway maps and the BRITE hierarchies. This enables an integrated analysis of drug interactions with genomic information.
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1599:
1538:
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271:. It integrates building blocks and wiring diagrams of the system—more specifically, genetic building blocks of genes and proteins, chemical building blocks of
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240:, he started developing the KEGG PATHWAY database. It is a collection of manually drawn KEGG pathway maps representing experimental knowledge on
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The KEGG metabolic pathway maps are drawn to represent the dual aspects of the metabolic network: the genomic network of how genome-encoded
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in the form of establishing correspondences to the wiring diagrams of KEGG pathway maps, KEGG modules, and BRITE hierarchies.
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in Japan, the US, and Europe. They are distinguished by chemical structures and/or chemical components and associated with
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individual entries in the other databases of KEGG. The pathway maps are classified into the following sections:
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Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M (2006).
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identified in the metabolome will lead to the understanding of enzymatic pathways and enzyme genes involved.
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Several months after the KEGG project was initiated in 1995, the first report of the completely sequenced
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are connected to catalyze consecutive reactions and the chemical network of how chemical structures of
252:. Each pathway map contains a network of molecular interactions and reactions and is designed to link
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1142:"The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection"
1001:
Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, Hamajima M, Kawasaki T, Kanehisa M (2006).
236:. Foreseeing the need for a computerized resource that can be used for biological interpretation of
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International
Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics
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genome was published. Since then all published complete genomes are accumulated in KEGG for both
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features, so that they can be used for automatic interpretation of genome and metagenome data.
214:
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643:
404:
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Kanehisa M (2013). "Chemical and genomic evolution of enzyme-catalyzed reaction networks".
857:
233:
8:
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1371:
1093:"KEGG for representation and analysis of molecular networks involving diseases and drugs"
1044:"Modular architecture of metabolic pathways revealed by conserved sequences of reactions"
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Microsoft
Research - University of Trento Centre for Computational and Systems Biology
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Another database that supplements KEGG PATHWAY is the KEGG BRITE database. It is an
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800:"Data, information, knowledge and principle: back to metabolism in KEGG"
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According to the developers, KEGG is a "computer representation" of the
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Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M (2014).
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Muto A, Kotera M, Tokimatsu T, Nakagawa Z, Goto S, Kanehisa M (2013).
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618:- CTD integrates KEGG pathways with toxicogenomic and disease data
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Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M (2010).
748:"From genomics to chemical genomics: new developments in KEGG"
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African
Society for Bioinformatics and Computational Biology
846:
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Max Planck
Institute of Molecular Cell Biology and Genetics
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308:
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182:
133:
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Kanehisa M (1997). "A database for post-genome analysis".
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BRITE: hierarchical classifications of biological entities
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International
Nucleotide Sequence Database Collaboration
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954:"LIGAND database for enzymes, compounds and reactions"
115:
77:
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potentials of the organism. Alternatively, a set of
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These correspondences are made using the concept of
228:, professor at the Institute for Chemical Research,
224:The KEGG database project was initiated in 1995 by
193:research and education, including data analysis in
1310:, database of protein sequences grouping together
42:Bioinformatics resource for deciphering the genome
1865:
1545:US National Center for Biotechnology Information
1630:International Society for Computational Biology
664:"KEGG: Kyoto Encyclopedia of Genes and Genomes"
1697:ISCB Africa ASBCB Conference on Bioinformatics
793:
791:
1644:Institute of Genomics and Integrative Biology
1259:
1673:European Conference on Computational Biology
1191:"Popular plant database set to charge users"
1133:
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290:MODULE: modules or functional units of genes
169:) is a collection of databases dealing with
1708:Research in Computational Molecular Biology
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1685:International Conference on Bioinformatics
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287:maps for cellular and organismal functions
1679:Intelligent Systems for Molecular Biology
1165:
1140:Galperin MY, Fernández-Suárez XM (2012).
1116:
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1018:
977:
920:
823:
771:
687:
1003:"KEGG as a glycome informatics resource"
1667:Basel Computational Biology Conference‎
952:Goto S, Nishioka T, Kanehisa M (1999).
522:
322:groups of genes in the complete genomes
167:Kyoto Encyclopedia of Genes and Genomes
1866:
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418:Environmental information processing (
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16:Collection of bioinformatics databases
1624:International Society for Biocuration
1522:European Molecular Biology Laboratory
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209:studies, modeling and simulation in
1650:Japanese Society for Bioinformatics
616:Comparative Toxicogenomics Database
244:and various other functions of the
13:
1612:European Molecular Biology network
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232:, under the then ongoing Japanese
14:
1905:
1702:Pacific Symposium on Biocomputing
1606:Australia Bioinformatics Resource
1573:Swiss Institute of Bioinformatics
1556:Netherlands Bioinformatics Centre
1516:European Bioinformatics Institute
1220:
1845:
1834:
1833:
1504:Database Center for Life Science
1492:Computational Biology Department
1380:Arabidopsis Information Resource
597:of all marketed drugs in Japan.
572:The KEGG DRUG database contains
399:Genetic information processing (
25:
1350:Specialised genomic databases:
1551:Japanese Institute of Genetics
560:, in addition to metabolites.
1:
1471:Rosalind (education platform)
1388:Zebrafish Information Network
1356:Saccharomyces Genome Database
913:10.1016/j.febslet.2013.06.026
725:10.1016/S0168-9525(97)01223-7
649:
373:and health-related substances
1879:Genetic engineering in Japan
1801:List of biological databases
1320:Protein Information Resource
810:(Database issue): D199–205.
379:
7:
1294:European Nucleotide Archive
1103:(Database issue): D355–60.
662:Kanehisa M, Goto S (2000).
609:
10:
1910:
1894:21st-century encyclopedias
758:(Database issue): D354–7.
1829:
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1579:Wellcome Sanger Institute
1533:J. Craig Venter Institute
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1203:10.1038/nature.2013.13642
340:REACTION, RPAIR, RCLASS:
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1562:Philippine Genome Center
1152:(Database issue): D1–8.
1806:Molecular phylogenetics
1302:China National GeneBank
870:10.1126/science.7542800
315:in the complete genomes
189:. KEGG is utilized for
1510:DNA Data Bank of Japan
1298:DNA Data Bank of Japan
215:translational research
1791:Computational biology
1306:Secondary databases:
1232:GenomeNet mirror site
1020:10.1093/glycob/cwj010
644:Gene Disease Database
327:Chemical information
78:Kanehisa Laboratories
1874:Biological databases
1288:Sequence databases:
970:10.1093/nar/27.1.377
586:metabolizing enzymes
523:Chemical information
444:Organismal systems (
429:Cellular processes (
298:Genomic information
280:Systems information
238:genome sequence data
234:Human Genome Program
1584:Whitehead Institute
1372:Rat Genome Database
1189:Hayden, EC (2013).
1158:10.1093/nar/gkr1196
862:1995Sci...269..496F
816:10.1093/nar/gkt1076
680:10.1093/nar/28.1.27
519:procedure in KEGG.
488:Genomic information
424:signal transduction
385:Systems information
354:Health information
348:enzyme nomenclature
187:chemical substances
175:biological pathways
21:
1821:Sequence alignment
1528:Flatiron Institute
1109:10.1093/nar/gkp896
764:10.1093/nar/gkj102
601:Subscription model
574:active ingredients
564:Health information
420:membrane transport
342:chemical reactions
332:chemical compounds
330:COMPOUND, GLYCAN:
19:
1861:
1860:
1816:Sequence database
1330:Protein Data Bank
1324:Other databases:
1146:Nucleic Acids Res
1097:Nucleic Acids Res
1060:10.1021/ci3005379
958:Nucleic Acids Res
856:(5223): 496–512.
804:Nucleic Acids Res
752:Nucleic Acids Res
668:Nucleic Acids Res
517:genome annotation
301:GENOME: complete
269:biological system
256:in the genome to
160:
159:
1901:
1884:Online databases
1849:
1848:
1837:
1836:
1796:List of biobanks
1760:Stockholm format
1568:Scripps Research
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466:Drug development
450:endocrine system
441:functions, etc.)
230:Kyoto University
219:drug development
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84:Primary citation
68:Kyoto University
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357:DISEASE: human
273:small molecules
226:Minoru Kanehisa
211:systems biology
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63:Research center
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1106:
1102:
1098:
1094:
1087:
1079:
1075:
1070:
1065:
1061:
1057:
1054:(3): 613–22.
1053:
1049:
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1038:
1030:
1026:
1021:
1016:
1012:
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997:
989:
985:
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677:
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669:
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632:
629:
628:Gene Ontology
626:
623:
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598:
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583:
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446:immune system
443:
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439:cell membrane
436:
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401:transcription
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258:gene products
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55:
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23:
1850:
1838:
1745:Nexus format
1740:NeXML format
1735:FASTQ format
1730:FASTA format
1718:File formats
1480:Institutions
1341:
1227:KEGG website
1194:
1184:
1149:
1145:
1135:
1100:
1096:
1086:
1051:
1047:
1037:
1010:
1007:Glycobiology
1006:
996:
964:(1): 377–9.
961:
957:
947:
904:
900:
894:
853:
849:
842:
807:
803:
755:
751:
741:
719:(9): 375–6.
716:
713:Trends Genet
712:
706:
674:(1): 27–30.
671:
667:
657:
604:
571:
567:
554:
542:biosynthetic
526:
510:
491:
478:
470:
388:
266:
223:
203:metabolomics
199:metagenomics
166:
162:
161:
98:Release date
1725:CRAM format
1646:(CSIR-IGIB)
1240:in MetaBase
922:2433/178762
590:Crude drugs
584:molecules,
558:xenobiotics
550:metabolites
506:annotations
502:prokaryotes
431:cell growth
409:replication
405:translation
371:crude drugs
318:ORTHOLOGY:
155:KEGG Mapper
128:Web service
39:Description
1868:Categories
1811:Sequencing
1775:GTF format
1770:GFF format
1765:VCF format
1755:SAM format
1518:(EMBL-EBI)
1444:SOAP suite
1364:VectorBase
1326:BioNumbers
1312:Swiss-Prot
650:References
533:substrates
498:eukaryotes
474:phenotypic
435:cell death
395:Metabolism
242:metabolism
205:and other
74:Laboratory
1638:(ISCB-SC)
1608:(EMBL-AR)
1541:(MPI-CBG)
1282:Databases
1211:211729309
901:FEBS Lett
513:orthologs
494:bacterial
380:Databases
369:ENVIRON:
283:PATHWAY:
48:Organisms
1840:Category
1710:(RECOMB)
1660:Meetings
1614:(EMBnet)
1464:Server:
1439:SAMtools
1434:PANGOLIN
1397:Software
1376:PHI-base
1368:WormBase
1338:InterPro
1176:22144685
1127:19880382
1078:23384306
1029:16014746
939:40074657
931:23816707
886:10423613
834:24214961
782:16381885
698:10592173
610:See also
537:products
481:ontology
461:diseases
359:diseases
346:ENZYME:
320:ortholog
313:proteins
262:proteins
260:(mostly
250:organism
248:and the
195:genomics
179:diseases
138:KEGG API
92:10592173
1852:Commons
1687:(InCoB)
1632:(ISCB)
1620:(INSDC)
1602:(ASBCB)
1506:(DBCLS)
1500:(COSBI)
1414:Clustal
1360:FlyBase
1334:Ensembl
1308:UniProt
1290:GenBank
1167:3245068
1118:2808910
1069:3632090
988:9847234
878:7542800
858:Bibcode
850:Science
825:3965122
773:1347464
733:9287494
639:Uniprot
529:enzymes
456:, etc.)
426:, etc.)
415:, etc.)
336:glycans
307:GENES:
303:genomes
285:pathway
171:genomes
111:Website
57:Contact
34:Content
1693:(CIBB)
1681:(ISMB)
1675:(ECCB)
1652:(JSBi)
1558:(NBIC)
1547:(NCBI)
1535:(JCVI)
1524:(EMBL)
1512:(DDBJ)
1466:ExPASy
1449:TopHat
1429:MUSCLE
1419:EMBOSS
1409:Bowtie
1384:GISAID
1344:, and
1316:TrEMBL
1209:
1195:Nature
1174:
1164:
1125:
1115:
1076:
1066:
1027:
986:
979:148189
976:
937:
929:
884:
876:
832:
822:
780:
770:
731:
696:
689:102409
686:
634:PubMed
582:target
459:Human
413:repair
363:DRUG:
213:, and
185:, and
106:Access
90:
1704:(PSB)
1626:(ISB)
1575:(SIB)
1564:(PGC)
1494:(CBD)
1458:Other
1424:HMMER
1404:BLAST
1207:S2CID
935:S2CID
882:S2CID
309:genes
254:genes
207:omics
183:drugs
144:Tools
118:.kegg
1386:and
1352:BOLD
1342:KEGG
1318:and
1300:and
1236:The
1172:PMID
1123:PMID
1074:PMID
1025:PMID
984:PMID
927:PMID
874:PMID
830:PMID
778:PMID
729:PMID
694:PMID
630:(GO)
544:and
535:and
500:and
411:and
334:and
311:and
246:cell
163:KEGG
136:see
134:REST
101:1995
88:PMID
20:KEGG
1199:doi
1162:PMC
1154:doi
1113:PMC
1105:doi
1064:PMC
1056:doi
1015:doi
974:PMC
966:doi
917:hdl
909:doi
905:587
866:doi
854:269
820:PMC
812:doi
768:PMC
760:doi
721:doi
684:PMC
676:doi
576:of
217:in
150:Web
130:URL
120:.jp
116:www
52:All
1870::
1669:()
1382:,
1378:,
1374:,
1370:,
1366:,
1362:,
1358:,
1354:,
1340:,
1336:,
1332:,
1328:,
1314:,
1296:,
1292:,
1205:.
1197:.
1193:.
1170:.
1160:.
1150:40
1148:.
1144:.
1121:.
1111:.
1101:38
1099:.
1095:.
1072:.
1062:.
1052:53
1050:.
1046:.
1023:.
1011:16
1009:.
1005:.
982:.
972:.
962:27
960:.
956:.
933:.
925:.
915:.
903:.
880:.
872:.
864:.
852:.
828:.
818:.
808:42
806:.
802:.
790:^
776:.
766:.
756:34
754:.
750:.
727:.
717:13
715:.
692:.
682:.
672:28
670:.
666:.
452:,
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433:,
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221:.
201:,
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181:,
177:,
173:,
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1178:.
1156::
1129:.
1107::
1080:.
1058::
1031:.
1017::
990:.
968::
941:.
919::
911::
888:.
868::
860::
836:.
814::
784:.
762::
735:.
723::
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678::
165:(
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