Microarray Gene Expression Database

In this paper we describe the basic design of a microarray gene expression database to help microarray users and their informatics teams set up their information services. The first version of the microarray database object model ArrayExpress, which is described here, was developed at the European Bioinformatics Institute (EBI) in collaboration with the German Cancer Research Centre (DKFZ) and posted on the Internet in November, 1999 (see (http //www.ebi.ac.uk/arrayexpress)). A relational database implementation maxd based on the ArrayExpress object model was conducted at the University of Manchester (http //bioinf.man.ac.uk/microarray/resources.html) and is widely used for microarray laboratory informatics support. 

There are currently no publicly available DNA chip expression databases, however the Microarray Gene Expression Database Group (MGED) [3] at the EBI aims to facilitate the creation of a gene expression data repository. 

Public repositories of microarray gene expression data have been developed to store the results of array experiments ArrayExpress (32) in Europe, Gene Expression Omnibus (GEO) in the United States (33), and the Center for Information Biology Gene Expression Database (CIBEX) (34) in Japan. Many journals already require an accession number (indicating that a data set has been submitted to one of these public databases) prior to publication. 

The MIAME standard was created by the Functional Genomics Data Society, formerly known as the Microarray Gene Expression Data Society (http // www.mged.org), as an effort to provide standards to specify all the information necessary to describe and interpret unambiguously the results of a microarray experiment (74). The standard defines the contents required for compliance reports but it does not specify the format in which this data should be presented. As a consequence there are a number of different file formats for representing this data, and each public and subscription database has adopted its own format. 

Microarray databases are repositories containing experimental microarray data, mainly microarray gene expression data. Microarray databases are used to store the results of finished experiments, and to make the data available to other users and applications, either directly or via user download. Microarray databases can fall into two distinct classes ... 

Parkinson, H., U. Sarkans, M. Shojatalab, N. Abeygunawardena, S. Contrino, R. Coulson, A. Fame, et al. 2005. ArrayExpress—A public repository for microarray gene expression data at the EBI. Nucleic Acids Res 33, Database Issue D553-5. 

For example, Imoto et al. (2003) introduced a statistical method for estimating a gene network based on both microarray gene expression data and various biological knowledge databases such as protein-protein and protein-DNA interaction. 

ArrayExpress Microarray gene expression data collection database http //www.ebi.ac.uk/arrayexpress... 

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