ArrayExpress update—simplifying data submissions

By N. Kolesnikov, Emma Hastings, M. Keays, O. Melnichuk, Y. Tang, Eleanor Williams, Miroslaw Dylag, N. Kurbatova, Marco Brandizi, Tony Burdett and 8 more. Nucleic Acids Res., 2014

700 citations recorded by the source corpus.

The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is an international functional genomics database at the European Bioinformatics Institute (EMBL-EBI) recommended by most journals as a repository for data supporting peer-reviewed publications. It contains data from over 7000 public sequencing and 42 000 array-based studies comprising over 1.5 million assays in total. The proportion of sequencing-based submissions has grown significantly over the last few years and has doubled in the last 18 months, whilst the rate of microarray submissions is growing slightly. All data in ArrayExpress are available in the MAGE-TAB format, which allows robust linking to data analysis and visualization tools and standardized analysis. The main development over the last two years has been the release of a new data submission tool Annotare, which has reduced the average submission time almost 3-fold. In the near future, Annotare will become the only submission route into ArrayExpress, alongside MAGE-TAB format-based pipelines. ArrayExpress is a stable and highly accessed resource. Our future tasks include automation of data flows and further integration with other EMBL-EBI resources for the representation of multi-omics data.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9bd6e1e5e2919a37ba84a1a1b3aea90d2972526f

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Expression Atlas: gene and protein expression across multiple studies and organisms (2017, methodology): “Expression Atlas uses microarray and RNA-Seq data sets from ArrayExpress (2), NCBI’s Gene Expression Omnibus (GEO) (3), European Nucleotide Archive (ENA) (4) as well as other sources.”
g:Profiler—a web server for functional interpretation of gene lists (2016 update) (2016, unknown): “The majority of published studies have been accumulated in databases like ArrayExpress (27) and Gene Expression Omnibus (28).”
Revealing protein–lncRNA interaction (2015, unknown): “A growing wealth of CLIP-Seq and RIP-Seq data sets is hosted in databases such as Gene Expression Omnibus (GEO) [118] or ArrayExpress [119].”
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments (2017, methodology): “ChIP-seq datasets were extracted from the Gene Expression Omnibus (GEO) (2), ArrayExpress (AE) (3) and ENCODE (5) databases.”
BioGPS: building your own mash-up of gene annotations and expression profiles (2015, methodology): “We expanded the collection further by including ∼ 6000 datasets from EBI’s ArrayExpress repository (12).”
The PRIDE database and related tools and resources in 2019: improving support for quantification data (2018, background): “The aim is to improve the capture of the experimental design information and technical metadata (e.g. search parameters and relevant information contained in the raw files) (28,38).”
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).”
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data (2015, methodology): “Raw CHi-C, Hi-C and random ligation control data used in this study are available in ArrayExpress [54, 55] under accession numbers E-MTAB-2323 (GM12878) and EMTAB-2414 (mESC), respectively.”
jPOSTrepo: an international standard data repository for proteomes (2016, background): “In order to ensure reliability of the data and the capacity for re-analysis in the future, it is necessary to construct a high-quality public data repository for promising datasets (2), similar to the public data repositories for DNA sequences (3,4) and gene expression profiles (5,6).”
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond (2015, methodology): “There are several HT-dedicated repositories and resources of microbial experimental results, such as TBDB (27), CollectTF (28) and RegTransBase (29), which hold curated motif data from HTs sources with links to GEO from NCBI (30) and to ArrayExpress from EMBL-EBI (31); databases with expression prof”