New approach for understanding genome variations in KEGG

New approach for understanding genome variations in KEGG

2019 | Minoru Kanehisa¹, Yoko Sato², Miho Furumichi¹, Kanae Morishima¹ and Mao Tanabe¹
KEGG is a comprehensive knowledge base for biological interpretation of genome sequences and high-throughput data. It includes three generic categories: systems, genomic, and chemical information, plus a human-specific health information category. KEGG pathway maps, BRITE hierarchies, and KEGG modules are used to represent conserved features of cellular processes. However, the generic approach was inadequate for representing variations in human genomes, especially disease-related variations. To address this, a new approach was introduced where human gene variants are explicitly incorporated into 'network variants' in the KEGG NETWORK database. This allows accumulation of knowledge about disease-related perturbed molecular networks caused by gene variants, viruses, environmental factors, and drugs. KEGG NETWORK is a human-specific database that provides a more detailed picture of human diseases in terms of network-disease associations. It includes network variants for cancers, viral infections, and certain endocrine and metabolic diseases. The database contains network elements, where both reference and variant elements are manually created from published literature. Reference elements are represented by human gene IDs, while variant elements may include gene variants, viral proteins, environmental factors, and drugs. The network variation map is color-coded to indicate reference elements, gene variants, viral proteins, and drugs. The KEGG NETWORK database also contains drug-target relationships, especially for drugs with variant proteins as targets. The KEGG database has undergone several updates, including the KO system updates and improvements to the disease and drug databases. The KO system is a hierarchical classification of KO entries representing functional classification of genes and proteins. The KEGG ENZYME database implements the Enzyme Nomenclature with additional information about sequence data for enzymes. The disease and drug databases have been updated to include variant IDs, drug labels, and ICD-11 codes for diseases. KEGG is accessible via the KEGG main site and the GenomeNet mirror site. The content of KEGG IDs can be retrieved by entering an ID into the search box at the top page of either site.KEGG is a comprehensive knowledge base for biological interpretation of genome sequences and high-throughput data. It includes three generic categories: systems, genomic, and chemical information, plus a human-specific health information category. KEGG pathway maps, BRITE hierarchies, and KEGG modules are used to represent conserved features of cellular processes. However, the generic approach was inadequate for representing variations in human genomes, especially disease-related variations. To address this, a new approach was introduced where human gene variants are explicitly incorporated into 'network variants' in the KEGG NETWORK database. This allows accumulation of knowledge about disease-related perturbed molecular networks caused by gene variants, viruses, environmental factors, and drugs. KEGG NETWORK is a human-specific database that provides a more detailed picture of human diseases in terms of network-disease associations. It includes network variants for cancers, viral infections, and certain endocrine and metabolic diseases. The database contains network elements, where both reference and variant elements are manually created from published literature. Reference elements are represented by human gene IDs, while variant elements may include gene variants, viral proteins, environmental factors, and drugs. The network variation map is color-coded to indicate reference elements, gene variants, viral proteins, and drugs. The KEGG NETWORK database also contains drug-target relationships, especially for drugs with variant proteins as targets. The KEGG database has undergone several updates, including the KO system updates and improvements to the disease and drug databases. The KO system is a hierarchical classification of KO entries representing functional classification of genes and proteins. The KEGG ENZYME database implements the Enzyme Nomenclature with additional information about sequence data for enzymes. The disease and drug databases have been updated to include variant IDs, drug labels, and ICD-11 codes for diseases. KEGG is accessible via the KEGG main site and the GenomeNet mirror site. The content of KEGG IDs can be retrieved by entering an ID into the search box at the top page of either site.
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