ArrayExpress—a public repository for microarray gene expression data at the EBI

By H. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, Niran Abeygunawardena, S. Contrino, R. Coulson, Anna Farne, Gonzalo Garcia Lara, Ele Holloway, M. Kapushesky and 8 more. Nucleic Acids Res., 2004

1,203 citations recorded by the source corpus.

ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Informa-tion About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from ∼12 000 hybridizations covering 35 species. Data can be submitted online or directly from local databases or LIMS in a standard format, and password-protected access to prepublication data is provided for reviewers and authors. The data can be retrieved by accession number or queried by vari-ous parameters such as species, author and array platform. A facility to query experiments by gene and sample properties is provided for a growing subset of curated data that is loaded in to the ArrayExpress data warehouse. Data can be visualized and analysed using Expression Profiler, the integrated data analysis tool. ArrayExpress is available at http://www.ebi.ac.uk/arrayexpress.

Subfields: Molecular Biology

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Citations in the corpus

• Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures (2010, methodology): “Data downloaded from Array Express (20): imatinib treatment in leukemia patients, E-MEXP-433 (21).”
• Batch Effect Confounding Leads to Strong Bias in Performance Estimates Obtained by Cross-Validation (2014, background): “Largely facilitated by online repositories such as Gene Expression Omnibus (http://www.ncbi. nlm.nih.gov/geo /[1]) and ArrayExpress (http://www.ebi.ac.uk/ arrayexpress/[2]), many of these data sets are made freely available for other researchers to use.”
• NASCArrays: a repository for microarray data generated by NASC's transcriptomics service (2004, methodology): “Currently data are donated in MAGE-ML (9) format to `ArrayExpress (10)', the European Bioinformatics Institute's microarray database, where it will be further distributed to GEO at the NCBI (11).”
• Direct multiplexed measurement of gene expression with color-coded probe pairs (2008, methodology): “The array and NanoString data have been made public via the Array Express database (E-MEXP-1072”
• Integrative analysis of the cancer transcriptome (2005, background): “GEO (Gene Expression Omnibus), which has emerged as one of the principal repositories for microarray dat”
• Key Issues in Conducting a Meta-Analysis of Gene Expression Microarray Datasets (2008, methodology): “uk/arrayexpress/ [44]”
• Sharing Detailed Research Data Is Associated with Increased Citation Rate (2007, background): “Most data sets were located on lab websites (28), with a few found on publisher websites (4), or within public databases (6 in the Stanford Microarray Database (SMD)[8], 6 in Gene Expression Omnibus (GEO)[9], 2 in ArrayExpress[10], 2 in the NCI GeneExpression Data Portal (GEDP)(gedp.nci.nih.gov); so”
• The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology (2004, background): “For these reasons, public repositories of microarray data such as ArrayExpress ( 21 ) actively encourage users to provide GO annotation in the array design, to facilitate clustering of data according to the GO ontologies and to allow cross-platform data comparisons.”
• ArrayExpress update—simplifying data submissions (2014, background): “Established in 2003 (1), the ArrayExpress Archive of Functional Genomics Data (2) has become one of the major international repositories for microarray and highthroughput sequencing (HTS)-based functional genomics experiments.”
• Marker-Assisted Plant Breeding: Principles and Practices (2015, background): “UK, and is accessible to the public (Brazma et al. 2003; Parkinson et al. 2005).”
• PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments (2006, background): “Many of these microarray experiments have been deposited in array databases and are available for public scrutinizing and data mining purposes [1-3].”
• The minimum information about a proteomics experiment (MIAPE) (2007, methodology): “(1) Data and metadata are generated by an experiment; (2) some form of software collects the data and metadata, either by importing from computer-controlled instruments or from manual data entry; (3) MIAPE specifies the data and metadata to be requested by the software tool; (4) a controlled vocabul”
• Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. (2007, background): “Microarray repositories, such as GEO and ArrayExpress [2,3], and journal requirements to deposit microarray data before publication have begun to ameliorate this problem; however, it remains difficult to ask targeted biologic questions of the collective transcriptome data set.”