title: Data storage and analysis in ArrayExpress and Expression Profiler.
abstract: 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.
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors.forename: Gabriella
authors.initials: G
authors.lastname: Rustici
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors.forename: Misha
authors.initials: M
authors.lastname: Kapushesky
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors.forename: Nikolay
authors.initials: N
authors.lastname: Kolesnikov
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors.forename: Helen
authors.initials: H
authors.lastname: Parkinson
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors.forename: Ugis
authors.initials: U
authors.lastname: Sarkans
authors.affiliation: European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
authors.forename: Alvis
authors.initials: A
authors.lastname: Brazma
mesh_terms: 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