The KEGG resource for deciphering the genome
The KEGG resource for deciphering the genome
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DOI：
10.1093/nar/gkh063
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Hattori, M
中科院分区：
文献类型：
--
作者：
Kanehisa, M;Goto, S;Hattori, M
后基因组时代的一个重大挑战是对细胞和生物体进行完整的计算机表征，这将能够从基因组信息对细胞过程和生物体行为的更高层次复杂性进行计算机预测。为此，我们一直在开发一种基于知识的网络预测方法，即给定基因组中的一套完整基因，预测负责各种细胞过程的蛋白质相互作用网络。网址为http://www.genome.ad.jp/kegg/的KEGG是一个参考知识库，它整合了关于分子相互作用网络（如通路和复合物，PATHWAY数据库）的现有知识、基因组计划所产生的基因和蛋白质信息（GENES/SSDB/KO数据库）以及生化化合物和反应的信息（COMPOUND/GLYCAN/REACTION数据库）。这三种类型的数据库实际上代表了三个图形对象，分别称为蛋白质网络、基因全集和化学全集。目前正在做出新的努力，通过计算机和人工方式提取关于KO（KEGG直系同源）数据库中直系同源簇的知识，并收集和分析GLYCAN数据库中的碳水化合物结构。
A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a knowledge-based approach for network prediction, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes. KEGG at http://www.genome.ad.jp/kegg/ is the reference knowledge base that integrates current knowledge on molecular interaction networks such as pathways and complexes (PATHWAY database), information about genes and proteins generated by genome projects (GENES/SSDB/KO databases) and information about biochemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases). These three types of database actually represent three graph objects, called the protein network, the gene universe and the chemical universe. New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database.