Biological Knowledge Based on Genome Information

虽然许多生物体的完整基因组序列以及人类基因组的筏序列已经确定，但每个基因组中大约一半基因的功能特性还没有得到很好的表征。本项目旨在发展生物信息学技术，从基因组信息中了解细胞或生物体的高级功能意义和用途。具体而言，（1）我们开发了一个名为KEGG的参考数据库，其中包含有关蛋白质相互作用网络的现有知识，如代谢途径，各种调节途径和分子复合物。我们对50多个物种的基因组进行了蛋白质网络和相关细胞功能的预测。(2)我们开发了信息技术，从科学文献的文本中提取蛋白质名称和蛋白质-蛋白质相互作用的知识。(3)我们开发了信息技术来分析基因表达谱数据，例如用于检测共表达簇和预测基因调控网络。(4)我们继续开发疾病相关基因的突变数据库。该项目有助于进一步发展作为日本生物医学研究信息学基础设施的GenomeNet数据库服务，并通过定期组织讲习班和辅导，培养生物信息学研究界。基本研究成果以及KEGG等实用数据库产品可在GenomeNet（http：//www.example.com）上免费查阅。www.genome.ad.jp

While the complete genome sequences of a number of organisms, as well as the raft sequences of the human genome, have already been determined, functional properties are not well characterized for roughly a half of the genes in each genome. This project aimed at developing bioinformatics technologies for understanding hihgher order functional meanings and utilities of the cell or the organism from its genome information. Specifically, (1) we developed a reference database named KEGG, which contains current knowledge on protein interaction networks such as metabolic pathways, various regulatory pathways, and molecular complexes. We performed prediction of protein networks and associated cellular functions for the genomes of over 50 species. (2) We developed information technology to extract knowledge on protein names and protein-protein interactions from the text in scientific literature. (3) We developed information technology to analyze gene expression profile data, such as for detecting coexpression clusters and for predicting gene regulatory networks. (4) We continued to develop mutation database for disease related genes. The project has been instrumental in further developing the GenomeNet database service as the informatics infrastructure for biomedical research in Japan and in nurturing the bioinformatics research community by regularly organizing workshops and tutorials. The basic research results, as well as the practical database products such as KEGG, are freely made available at the GenomeNet (http://www.genome.ad.jp).