Genome-level integration of gene functional information and its application to elucidation of gene systems

基因功能信息的基因组水平整合及其在阐明基因系统中的应用

基本信息

批准号：
15011229
负责人：
MATSUDA Hideo
金额：
$ 20.48万
依托单位：
Osaka University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research on Priority Areas
财政年份：
2003
资助国家：
日本
起止时间：
2003 至 2004
项目状态：
已结题

项目摘要

Although a large amount of data about genes from the genomes of many organisms has been obtained, the filmdom of many genes are still uncharacterized. This was due to the facts that the information of gene functions were not systematically arranged and not easily utilized, and the method for classifying genes to the gene families of functionally-coupled groups with their sequence homologies or expression similarities. To cope with these issues, this study aims to elucidate gene systems focusing on gene interactions by developing methods for systematic extraction of clearly-characterized gene functions and systematic arrangement of the extracted functional information in genome level.The achievements of this study are:(1) More accurate inference of gene regulatory networks with Bayesian network from gene expression data by using the functional classification of Gene Ontology as well as expression similarity.(2) Mapping genes on microarrays onto the KEGG metabolic pathway database, construction of the system for analyzing the genes with their microarray data, the computational analysis of the tryptophan degradation pathway in mouse and the prediction of the existence of an alternative pathway.(3) Development of analysis pipeline called SayaMatcher for finding the transcription-factor binding sites of which number is expected as several thousands to several hundreds of thousands.(4) Construction of a DAS (Distributed Annotation System) server that makes it possible to display and browse those found binding sites and their positions on the genome.

尽管已经获得了许多生物基因组的大量有关基因的数据，但许多基因的摄影仍然没有表征。这是由于事实是，基因函数的信息不是系统排列的，也不容易使用，以及将基因与功能偶联基团的基因家族分类的方法与其序列同源性或表达相似性。为了应对这些问题，本研究旨在通过开发针对基因相互作用的基因系统，通过开发系统提取清晰特征的基因功能的系统提取方法和在基因组水平上提取的功能信息的系统排列，该研究的成就是：（1）（1）通过对基因网络的表达性进行更准确的划分，以表达基因网络，以表达基因网络，以表达基因网络，从而表达贝叶斯网络，从而将贝叶斯网络用于贝叶斯网络，从而使用贝叶斯网络，以实现贝雷斯网络。 similarity.(2) Mapping genes on microarrays onto the KEGG metabolic pathway database, construction of the system for analyzing the genes with their microarray data, the computational analysis of the tryptophan degradation pathway in mouse and the prediction of the existence of an alternative pathway.(3) Development of analysis pipeline called SayaMatcher for finding the transcription-factor binding sites of which number is expected as several thousands to several hundreds （4）构建DAS（分布式注释系统）服务器，该服务器可以显示和浏览那些发现的绑定位点及其在基因组上的位置。

项目成果

期刊论文数量（94）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Architecture of a Grid-Enabled Research Platform with Location-Transparency for Bioinformatics

具有位置透明性的生物信息学网格研究平台的架构

DOI：
发表时间：
2005
期刊：
Lecture Notes in Bioinformatics 3370
影响因子：
0
作者：
Y.Tohsato;T.Kosaka;S.Date;S.Shimojo;H.Matsuda
通讯作者：
H.Matsuda

H.Kawaji, et al.: "Graph-based clustering for finding distant relationships in a large set of protein sequences"Bioinformatics. 20・2. 243-252 (2004)

H. Kawaji 等人：“基于图的聚类，用于在大量蛋白质序列中查找远距离关系”，生物信息学 20・2（2004 年）。

DOI：
发表时间：
期刊：
影响因子：
0
作者：
通讯作者：

Introduction to the practical analysis of DNA microarray data

DNA 微阵列数据的实用分析简介

DOI：
发表时间：
2003
期刊：
Tanpakushitsu Kakusan Koso. 48(2)
影响因子：
0
作者：
Bono H;Nakao MC.
通讯作者：
Nakao MC.

Mouse proteome analysis

DOI：
10.1101/gr.978703
发表时间：
2003-06-01
期刊：
GENOME RESEARCH
影响因子：
7
作者：
Kanapin, A;Batalov, S;Yuan, Z
通讯作者：
Yuan, Z

SayaMatcher : genome scale organization and systematic analysis of nuclear receptor response elements

SayaMatcher：核受体反应元件的基因组规模组织和系统分析

DOI：
发表时间：
2005
期刊：
Gene 364
影响因子：
0
作者：
Takeuchi;Yukari;竹内由香里;Jieun Cheong;Kenji Watanabe et al.;Kento Koketsu et al.;Hiroki Oguri et al.;Yuta Fujita et al.;Yuta Fujita et al.;Hiroki Oguri et al.;Hiroki Oguri et al.;Nakazato T.;坊農秀雅;Bono H
通讯作者：
Bono H