GIMS: an integrated data storage and analysis environment for genomic and functional data

被引:30
作者
Cornell, M
Paton, NW
Hedeler, C
Kirby, P
Delneri, D
Hayes, A
Oliver, SG
机构
[1] Univ Manchester, Sch Biol Sci, Manchester M13 9PL, Lancs, England
[2] Univ Manchester, Dept Comp Sci, Manchester M13 9PL, Lancs, England
关键词
genome database; Saccharomyces cerevisiae; transcriptome analysis;
D O I
10.1002/yea.1047
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Effective analyses in functional genomics require access to many kinds of biological data. For example, the analysis of upregulated genes in a microarray experiment might be aided by information concerning protein interactions or proteins' cellular locations. However, such information is often stored in different formats at different sites, in ways that may not be amenable to integrated analysis. The Genome Information Management System (GIMS) is an object database that integrates genomic data with data on the transcriptome, protein-protein interactions, metabolic pathways and annotations, such as gene ontology terms and identifiers. The resulting system supports the running of analyses over this integrated data resource, and provides comprehensive facilities for handling and interrelating the results of these analyses. GIMS has been used to store Saccharomyces cerevisiae data, and we demonstrate how the integrated storage of diverse types of data can be beneficial for analysis, using combinations of complex queries. As an example, we describe how GIMS has been used to analyse a collection of aryl alcohol dehydrogenase gene deletion mutants. The GIMS database can be accessed remotely using a Java application that can be downloaded from http://img.cs.man.ac.uk/gims. Copyright (C) 2003 John Wiley Sons, Ltd.
引用
收藏
页码:1291 / 1306
页数:16
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