A Comparison of Microarray Databases
M Gardiner-Garden, TG Littlejohn
Briefings in Bioinformatics, 2(2): 143-158 (2001).
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.