ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression

By H. Parkinson, M. Kapushesky, N. Kolesnikov, G. Rustici, Mohammadreza Shojatalab, Niran Abeygunawardena, Hugo Bérubé, Miroslaw Dylag, Ibrahim Emam, Anna Farne and 24 more. Nucleic Acids Res., 2008

457 citations recorded by the source corpus.

ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository—a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse—a database of gene expression profiles and other bio-measurements and the ArrayExpress Atlas—a new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions. The Repository contains data from over 6000 experiments comprising approximately 200 000 assays, and the database doubles in size every 15 months. The majority of the data are array based, but other data types are included, most recently—ultra high-throughput sequencing transcriptomics and epigenetic data. The Warehouse and Atlas allow users to query for differentially expressed genes by gene names and properties, experimental conditions and sample properties, or a combination of both. In this update, we describe the ArrayExpress developments over the last two years.

Subfields: Molecular Biology

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Citations in the corpus

Cistrome: an integrative platform for transcriptional regulation studies (2011, background): “…such as the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) [33] and the European Bioinformatics Institute (EBI) ArrayExpress [34] host array data, and databases such as the NCBI Sequence Reads Archive (SRA) [35] and the EBI SRA host sequencing data [36].”
NCBI GEO: archive for functional genomics data sets—10 years on (2010, background): “It is for this reason that GEO and ArrayExpress have experienced remarkable growth.”
Reuse of public genome-wide gene expression data (2012, methodology): “To assess how archived gene expression data have recently been used, we analysed publications from 2011 that either tagged ‘ArrayExpress’ or cited any of the five ArrayExpress publications in the Nucleic Acid Research journal database issues 6,58,59,60,8 .”
Chemical Entities of Biological Interest: an update (2009, methodology): “We have also extended our automatic crossreference links to include annotated ChEBI identifiers within the ArrayExpress (11), BioModels (12), Reactome (13) and SABIO-RK (14) databases.”
The International Nucleotide Sequence Database Collaboration (2010, methodology): “The strategy adopted by INSDC has been the establishment of close collaborations with groups having specialized expertise, such as GEO (6) and ArrayExpress (7) for functional genomics experiments.”
Frozen robust multiarray analysis (fRMA). (2010, unknown): “, 2002) and ArrayExpress (Parkinson et al., 2008).”
The IntAct molecular interaction database in 2010 (2009, background): “Other options link to external sites, and allow the visualization of InterPro domains, the involvement of molecules in Reactome pathways, the chromosomal location of the originating gene in Ensembl, or links to mRNA expression with ArrayExpress (21).”
bc-GenExMiner: an easy-to-use online platform for gene prognostic analyses in breast cancer (2012, methodology): “We looked for publicly available breast cancer gene expression data sets with clinical information, including prognosis, in repositories such as Gene Expression Omnibus (GEO), ArrayExpress and Stanford microarray database, author’s individual web pages and in articles, selecting those with a medium ”
Molecular signatures database (MSigDB) 3.0 (2011, background): “0 include links to source datasets in Gene Expression Omnibus (GEO) (Barrett, 2009) and ArrayExpress (Parkinson, 2009).”
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes (2010, background): “The ‘Experimental data’ tab provides a starting point for identifying expression data studies and linking to respective data at NCBI’s Gene Expression Omnibus (20) or ArrayExpress (21) or to sequence read data at NCBI’s Trace Archive or Short Reads Archive (22).”
Mapping Identifiers for the Integration of Genomic Datasets with the R/Bioconductor package biomaRt (2009, methodology): “mRNA expression was measured using the Affymetrix U133a platform, and the CEL files are available at the ArrayExpress databas”