ArrayExpress update—trends in database growth and links to data analysis tools

By G. Rustici, N. Kolesnikov, Marco Brandizi, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, J. Ison, M. Keays and 16 more. Nucleic Acids Res., 2012

388 citations recorded by the source corpus.

The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting peer-reviewed publications. It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data. All data are available from ArrayExpress in MAGE-TAB format, which allows robust linking to data analysis and visualization tools, including Bioconductor and GenomeSpace. Additionally, R objects, for microarray data, and binary alignment format files, for sequencing data, have been generated for a significant proportion of ArrayExpress data.

Subfields: Molecular Biology

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Citations in the corpus

Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants (2015, methodology): “We would like to thank James Malone, Sirarat Sarntivijai, Drashtti Vasant and Catherine Leroy for their assistance in enriching EFO in terms needed to describe samples studied in Atlas, Nikolay Kolesnikov, Ahmed Ali for their help with the ArrayExpress interface and assistance in submissions of new ”
The Ontology for Biomedical Investigations (2016, background): “The workflow of the ISA system has been validated and is compatible with existing technology centric formats (e.g. MAGE-TAB for ArrayExpress [37] and Sequence Read Archive (SRA) EXtensible Markup Language (XML) for ENA [36], respectively).”
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.”
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data (2014, background): “DO has been incorporated into a growing number of biomedical resources including the EBI Array Express (23), the Neuroscience Information Network (NIFSTD) (24), Neurocarta (25), NeuroDevNet (26), Infectious Disease Ontology (http://infectiousdiseaseontology.”
The Database of Genomic Variants: a curated collection of structural variation in the human genome (2013, background): “Authors are encouraged to submit their raw data to the appropriate archive, either Gene Expression Omnibus (16) or Array Express (17) and processed variant calls to DGVa or dbVar.”
The Molecular Signatures Database (MSigDB) hallmark gene set collection (2015, neutral): “, 2007) and ArrayExpress (Rustici et al., 2013) to find relevant human, mouse, or rat expression datasets for each of the 73 clusters of the previous step.”
Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments (2013, methodology): “Subsequently, good quality microRNA RNA-sequencing experiments available in ArrayExpress will be re-processed and included in Expression Atlas.”
Big Data Application in Biomedical Research and Health Care: A Literature Review (2016, background): “The ArrayExpress Archive of Functional Genomics data repository 45,46 is an international collaboration for integrating high-throughput genomics data.”
Data integration in the era of omics: current and future challenges (2014, methodology): “An example is the Gene Expression Ombinus (GEO [8,9]); GEO (similarly to ArrayExpress [23]) is a data repository for microarray and NGS data that requires the data producers to submit data following the Minimum Information About a Microarray Experiment (MIAME) guidelines [24].”
Gateways to the FANTOM5 promoter level mammalian expression atlas (2015, background): “Thousands of studies have been published on gene expression profiles using microarrays (Gene Expression Omnibus [14], ArrayExpress [15], CIBEX [16]) and collections of curated data sets (GNF SymAtlas2 [17], EBI Gene expression atlas [18], BioGPS [19]) have become popular tools to survey gene express”
PATRIC, the bacterial bioinformatics database and analysis resource (2013, background): “There are thousands of gene expression datasets in the public repositories such as GEO (10) and ArrayExpress (11), and this number continues to grow.”
Unsupervised extraction of functional gene expression signatures in the bacterial pathogen Pseudomonas aeruginosa with eADAGE (2016, methodology): “A team of P. aeruginosa biologists annotated the media for all samples in the compendium by referring to information associated with each sample in the ArrayExpress (Rustici et al , 2013) and/or GEO (Edgar, 2002) databases and along with the original publication, if reported.”