ArrayExpress—a public database of microarray experiments and gene expression profiles

By H. Parkinson, M. Kapushesky, Mohammadreza Shojatalab, Niran Abeygunawardena, R. Coulson, Anna Farne, Ele Holloway, Nikolay Kolesnykov, P. Lilja, M. Lukk and 6 more. Nucleic Acids Res., 2006

744 citations recorded by the source corpus.

ArrayExpress is a public database for high throughput functional genomics data. ArrayExpress consists of two parts—the ArrayExpress Repository, which is a MIAME supportive public archive of microarray data, and the ArrayExpress Data Warehouse, which is a database of gene expression profiles selected from the repository and consistently re-annotated. Archived experiments can be queried by experiment attributes, such as keywords, species, array platform, authors, journals or accession numbers. Gene expression profiles can be queried by gene names and properties, such as Gene Ontology terms and gene expression profiles can be visualized. ArrayExpress is a rapidly growing database, currently it contains data from >50 000 hybridizations and >1 500 000 individual expression profiles. ArrayExpress supports community standards, including MIAME, MAGE-ML and more recently the proposal for a spreadsheet based data exchange format: MAGE-TAB. Availability: .

Subfields: Molecular Biology

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Citations in the corpus

Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. (2013, neutral): “Datasets The data sets used in this study are publicly available (ArrayExpress [Ancona et al., 2006; Parkinson et al., 2007; Wendt et al., 2006], Gene Expression Omnibus [Barrett et al.”
ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression (2008, methodology): “The ArrayExpress Warehouse of gene expression profiles was added in 2005 (3, 4 ), and currently it includes data from over 600 studies and 20 000 samples.”
Perturbation-response genes reveal signaling footprints in cancer gene expression (2016, methodology): “We then used those as query terms for public perturbation experiments in the ArrayExpress database (Parkinson et al. 2007) and included a total of 223 submissions and 573 experiments in our data set, where each experiment is a distinct comparison between basal and perturbed arrays.”
Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support (2008, methodology): “In addition to model organism databases, most microarray experiment databases can be searched by terms from the Gene Ontology [90], including ArrayExpress [91] and the Cancer gene expression database (CGED) [92].”
OpenML: networked science in machine learning (2014, background): “We are ‘mapping and mining’ just about every complex phenomenon in nature, including the brain [21; 15], the ocean [18], gene sequences, genetic variants in humans [12], and gene functions [31].”
Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures (2010, background): “Gene-expression information from microarray data repositories such as Gene-expression Omnibus (19) and ArrayExpress (53) as well as from more specialized resources such as the drug response profile database Cmap (10) can be readily converted to ranked list inputs for our program.”
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks (2008, background): “ArrayExpress (13) and Gene Expression Omnibus (GEO) (14) are public repositories for microarray data.”
expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform1[OPEN] (2016, background): “Samples are ordered by their High level stress-disease status: none (green), disease (yellow), abiotic (purple), and transgenic (orange). experiments, which have been better catalogued and compared (Zimmermann et al., 2004; Parkinson et al., 2007; Wagner et al., 2013).”
Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species (2008, methodology): “Bgee currently uses EST data from Unigene [14] and Affymetrix data retrieved from ArrayExpress [15].”
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 .”
PrognoScan: a new database for meta-analysis of the prognostic value of genes (2009, methodology): “Cancer microarray datasets with clinical annotation were intensively collected from the public domain including Gene Expression Omnibus (GEO) [8], ArrayExpress [9] and individual laboratory web sites, under the following criteria: 1) includes patient information on survival event and time, 2) contai”