Data storage and analysis in ArrayExpress and Expression Profiler.
ArrayExpress at the European Bioinformatics Institute is a public database for MIAME-compliant microarray and transcriptomics data. It consists of two parts: the ArrayExpress Repository, which is a public archive of microarray data, and the ArrayExpress Warehouse of Gene Expression Profiles, which contains additionally curated subsets of data from the Repository. Archived experiments can be queried by experimental attributes, such as keywords, species, array platform, publication details, or accession numbers. Gene expression profiles can be queried by gene names and properties, such as Gene Ontology terms, allowing expression profiles visualization. The data can be exported and analyzed using the online data analysis tool named Expression Profiler. Data analysis components, such as data preprocessing, filtering, differentially expressed gene finding, clustering methods, and ordination-based techniques, as well as other statistical tools are all available in Expression Profiler, via integration with the statistical package R.
Rustici
Gabriella
G
European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Kapushesky
Misha
M
European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Kolesnikov
Nikolay
N
European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Parkinson
Helen
H
European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Sarkans
Ugis
U
European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Brazma
Alvis
A
European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software