ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments

By H. Parkinson, Ugis Sarkans, N. Kolesnikov, Niran Abeygunawardena, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Ele Holloway and 12 more. Nucleic Acids Res., 2010

372 citations recorded by the source corpus.

The ArrayExpress Archive (http://www.ebi.ac.uk/arrayexpress) is one of the three international public repositories of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/98ab5e420fd1dc061f9be176ae40d38934f3ca58

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In Molecular Biology

1. Jaak Vilo
2. Alvis Brazma
3. Tambet Arak
4. Johan Rung
5. Tanya Barrett
6. Jüri Reimand
7. M. Kallio
8. Ann Nowé

Citations in the corpus

• ArrayExpress update – from bulk to single-cell expression data (2018, background): “Many of the new ArrayExpress developments since then have focused on optimizing our data submission and access interfaces to accommodate these types of data (3,4).”
• CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data (2013, background): “1b) can be compared with linear and non-linear interrelations derived from expression data from normal colon and colon tumors [E-MTAB-57 (Ancona et al ., 2006), E-GEOD-37892, ArrayExpress (Parkinson et al ., 2011)].”
• Batch effect removal methods for microarray gene expression data integration: a survey (2013, background): “…importance resides mainly in the potentially huge biological insights that could be discovered by analysing at the same time large numbers of genomic datasets available through public repositories such as Gene Expression Omnibus [2], ArrayExpress [3] or InSilicoDB (http://insilico.ulb .ac.be/) [4].”
• ArrayExpress update—trends in database growth and links to data analysis tools (2012, background): “The ArrayExpress Archive of Functional Genomics Data (1) is one of the major international repositories for functional genomics high throughput data, supporting publications as well as various data generating consortia.”
• The International Nucleotide Sequence Database Collaboration (2011, background): “Linkages may also be established between initiatives with data deposited in the INSDC sequence archives and repositories that house analysis of raw sequence output, such as GEO (4), ArrayExpress (5) and dbGaP.”
• NCBI GEO: archive for functional genomics data sets—update (2012, background): “Together with ArrayExpress (4), data for > 1 million samples are currently available in the public domain.”
• Chipster: user-friendly analysis software for microarray and other high-throughput data (2011, methodology): “Chipster can also export data in a suitable format for uploading to the ArrayExpress [8] and GEO [9] databases.”
• 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 .”
• RiceXPro Version 3.0: expanding the informatics resource for rice transcriptome (2012, background): “The rapid accumulation of rice microarray data in public repositories such as NCBI’s Gene Expression Omnibus (GEO) (16,17), EBI Array Express (18) and DDBJ CIBEX (19) also led to the development of informatics resources and analysis tools for integrating and extracting useful information on gene exp”
• g:Profiler—a web server for functional interpretation of gene lists (2011 update) (2011, positive): “It allows users to find similar gene expression profiles to their gene of interest in a large collection of public microarray datasets from ArrayExpress (23).”
• The sequence read archive: explosive growth of sequencing data (2011, neutral): “uk/arrayexpress) (6) and DDBJ Omics Archive (http://trace.”