A comparison of microarray databases

Abstract

Microarray technology has become one of the most important functional genomics technologies. A proliferation of microarray databases has resulted. It can be difficult for researchers exploring this technology to know which bioinformatics systems best meet their requirements. In order to obtain a better understanding of the available systems, a survey and comparative analysis of microarray databases was undertaken. The survey included databases that are currently available, as well as databases that should become available in early 2001. Databases fall into three categories: (i) those that can be installed locally, (ii) those available for public data submission and (iii) those available for public query. Developers of microarray gene-expression databases were asked questions regarding the scope and availability of their database, its system requirements, its future compliance with MGED (Microarray Gene Expression Database) standards, and its associated analytical tools. Participants included AMAD (Stanford/Berkeley/UCSF), ArrayExpress (EBI), ChipDB (MIT/Whitehead), GeneX (NCGR), GeNet (Silicon Genetics), GeneDirector (BioDiscovery), GEO (NCBI), GXD (Jackson Laboratory), mAdb (NCI), maxdSQL (University of Manchester), NOMAD (UCSF), RAD (University of Pennsylvania) and SMD (Stanford University). Other database developers were contacted but data was not available at the time of manuscript preparation. Each database fulfils a different role, reflecting the widely varying needs of microarray users.

Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks

“…These approaches cluster together genes irrespective of their function and without reference to the valuable amount of biological information available in public databases. An extensive list of such software, reviewed by Gardiner-Garden and Littlejohn (2001), can be found at: http://www.ncgr.org/genex/other_tools.html.…”

Comparison and meta-analysis of microarray data: from the bench to the computer desk

“…Currently, the only fully MIAME-supportive database is the ArrayExpress repository (http://www.ebi.ac.uk/ arrayexpress) [12], although other microarray databases are being developed so that they will eventually support MIAME [13,14]. Some journals already require publication of MIAME-compliant data to one of the two current repositories, ArrayExpress or Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) [15].…”

Application of Microarray Technology in Environmental and Comparative Physiology

“…The analysis of multiple sets of array data provides a huge amount of quantitative information, and analysis of the resulting deluge of data is a major challenge requiring extensive analytical tools. The management and storage of these data is the first component of the whole analysis process that has prompted the development of a number of microarray databases (35) and a proposal for the minimum amount of information that should be stored for each experiment to allow the data to be properly interpreted and independently verified (36).…”