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ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression
2009
Nucleic Acids Research
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Access and use of this website and the material on it are subject to the Terms and Conditions set forth at ArrayExpress update: from an archive of functional genomics experiments to the atlas of gene expression ...
http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository-a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse-a database ...
of in situ gene expression data and Tanya Barrett of GEO for assistance with SOFT to MAGE-TAB mapping. ...
doi:10.1093/nar/gkn889
pmid:19015125
pmcid:PMC2686529
fatcat:on7ynzj2jbb57cxrhuutikje5u
ArrayExpress update—simplifying data submissions
2014
Nucleic Acids Research
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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 ...
All data in ArrayExpress are available in the MAGE-TAB format, which allows robust linking to data analysis and visualization tools and standardized analysis. ...
ACKNOWLEDGEMENTS We would like to thank Simon Jupp, James Malone and Danielle Welter for the EFO work, and Marc Rosello, Rajesh Radhakrishnan and Rasko Leinonen for help in streamlining the flow of data ...
doi:10.1093/nar/gku1057
pmid:25361974
pmcid:PMC4383899
fatcat:c4fvlffcnfcpde7agoxjir4beu
ArrayExpress update – from bulk to single-cell expression data
2018
Nucleic Acids Research
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ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data from a variety of technologies assaying functional modalities of a genome, such as gene expression or promoter ...
Selected datasets are re-processed and loaded into our sister resource, the value-added Expression Atlas (and its component Single Cell Expression Atlas), which not only enables users to interpret the ...
ACKNOWLEDGEMENTS The authors would like to thank Juan Antonio Vicziano.
FUNDING ...
doi:10.1093/nar/gky964
pmid:30357387
pmcid:PMC6323929
fatcat:p2n5pu6dgffvtf3jp5ypftowxu
ArrayExpress update—trends in database growth and links to data analysis tools
2012
Nucleic Acids Research
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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 ...
It accepts data generated by sequencing or array-based technologies and currently contains data from almost a million assays, from over 30 000 experiments. ...
In addition to the data submitted directly to ArrayExpress, data from the Gene Expression Omnibus (GEO) (3) are imported to provide users with a single access to most of the functional genomics data available ...
doi:10.1093/nar/gks1174
pmid:23193272
pmcid:PMC3531147
fatcat:un6k6u4xqfdjpjt6yhdg5lf6de
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments
2010
Nucleic Acids Research
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The ArrayExpress Archive (http://www.ebi.ac.uk/ arrayexpress) is one of the three international public repositories of functional genomics data supporting publications. ...
The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. ...
The European Bioinformatics Institute's Gene Expression Atlas (GXA) (4) is now a separate resource from the Archive and is linked from the ArrayExpress Graphical User Interface. ...
doi:10.1093/nar/gkq1040
pmid:21071405
pmcid:PMC3013660
fatcat:4rn24k5lvzhajj4huiufljvsgy
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments
2011
Nucleic Acids Research
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The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive and the European Nucleotide Archive. ...
Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample ...
ACKNOWLEDGEMENTS In addition to the invaluable help from the entire Functional Genomics Team, led by Ugis Sarkans, we would like to thank particularly Ekaterina Pilicheva for help with gene re-annotation ...
doi:10.1093/nar/gkr913
pmid:22064864
pmcid:PMC3245177
fatcat:qi4tj2jmszh3zdkwmbwotggyo4
From ArrayExpress to BioStudies
2020
Nucleic Acids Research
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ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data at EMBL-EBI, established in 2002, initially as an archive for publication-related microarray data and was later ...
Over the last decade an increasing share of biological experiments involve multiple technologies assaying different biological modalities, such as epigenetics, and RNA and protein expression, and thus ...
INTRODUCTION ArrayExpress is an archive of functional genomics data, such as gene expression or DNA methylation profiling data (1) . ...
doi:10.1093/nar/gkaa1062
pmid:33211879
fatcat:p2nyf6ayibhvhif7hcsye7fu2a
Expression Atlas: gene and protein expression across multiple studies and organisms
2017
Nucleic Acids Research
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Novel features and visualizations include the on-the-fly analysis of gene set overlaps and the option to view gene co-expression in experiments investigating constitutive gene expression across tissues ...
As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants. ...
into ArrayExpress and European Nucleotide Archive; and our colleagues in Ensembl Genomes for the development of novel visualization of differential expression tracks from Atlas. ...
doi:10.1093/nar/gkx1158
pmid:29165655
pmcid:PMC5753389
fatcat:duqk25kctbauzihb22ieukvofa
Gene Expression Atlas at the European Bioinformatics Institute
2009
Nucleic Acids Research
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The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data. ...
The Gene Expression Atlas (http://www.ebi.ac .uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states ...
Sarkans on the gene reannotation pipeline; the work of Ugis Sarkans, Sergio Contrino and Hugo Berube on the earlier ArrayExpress Warehouse software served as a platform and motivation for the Atlas; Nikolay ...
doi:10.1093/nar/gkp936
pmid:19906730
pmcid:PMC2808905
fatcat:ruisihx4frgvbkwhmun2b6dyoy
ArrayExpress--a public database of microarray experiments and gene expression profiles
2007
Nucleic Acids Research
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Funding to pay the Open Access publication charges for this article was provided by the FELICS grant from the European Commission. ...
ACKNOWLEDGEMENTS The authors would like to acknowledge Patrick Kemmeren, Susanna-Assunta Sansone, Philippe Rocca-Serra, Catherine Brooksbank, Petteri Jokkinen and the EBI systems group and the ArrayExpress ...
The user can import data to Expression Profiler from the ArrayExpress advanced query interface by selecting 'Data Export to Expression Profiler', or can download zip archives from the ArrayExpress browse ...
doi:10.1093/nar/gkl995
pmid:17132828
pmcid:PMC1716725
fatcat:yrtu55lvzzci5j57beyijo2hhe
Expression Atlas update: from tissues to single cells
2019
Nucleic Acids Research
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With the increased availability of single cell RNA-Seq datasets in the public archives, we have now extended Expression Atlas with a new added-value service to display gene expression in single cells. ...
The website can be searched by genes within or across species to reveal experiments, tissues and cell types where this gene is expressed or under which conditions it is a marker gene. ...
Sarkans for their help with the ArrayExpress interface and assistance in submissions of new functional genomics studies to ArrayExpress. ...
doi:10.1093/nar/gkz947
pmid:31665515
pmcid:PMC7145605
fatcat:vp5gbm3mqbhjbhbucprqwyaggq
Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments
2013
Nucleic Acids Research
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for their support and guidance on the Expression Atlas production infrastructure and Nikolay Kolesnikov for his help with the ArrayExpress interface. ...
Finally, they would like to thank Misha Kapushesky and other previous developers of Gene Expression Atlas for their work and input, which will have inevitably influenced our efforts when developing its ...
High-quality microarray and RNA-sequencing data in Expression Atlas continues to come from ArrayExpress (2) , including data imported from GEO (3) . ...
doi:10.1093/nar/gkt1270
pmid:24304889
pmcid:PMC3964963
fatcat:bl7yghza35e55ivxrk7ojfnx5q
Transcriptomics and Epigenomics in head and neck cancer: available repositories and molecular signatures
2020
Cancers of the Head & Neck
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Finally, we highlighted the development and exploitation of three gene-expression signatures, whose clinical impact on prognosis/prediction of treatment response could be high. ...
The objective of the present review is to provide an overview on biological, prognostic and predictive molecular signatures in HNSCC. ...
The ArrayExpress archive is one of the ELIXIR Core Data Resources and stores data derived from array-and sequence-based experiments. ...
doi:10.1186/s41199-020-0047-y
pmid:31988797
pmcid:PMC6971871
fatcat:wydnloqnyff4pd2k62566viibe
Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants
2015
Nucleic Acids Research
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Since the last update, Atlas has grown sevenfold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell ...
For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons--estimated using consistent methodology across all ...
of novel visualisation of differential expression tracks from Atlas. ...
doi:10.1093/nar/gkv1045
pmid:26481351
pmcid:PMC4702781
fatcat:ejfwhmtlcvbz3guoi6pkyacyji
Expression Atlas update: gene and protein expression in multiple species
2021
Nucleic Acids Research
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The EMBL-EBI Expression Atlas is an added value knowledge base that enables researchers to answer the question of where (tissue, organism part, developmental stage, cell type) and under which conditions ...
The data are re-analyzed with the aim of reproducing the original conclusions of the underlying experiments. ...
Sarkans for their help with the Ar-rayExpress interface and assistance in submissions of new functional genomics studies to ArrayExpress. ...
doi:10.1093/nar/gkab1030
pmid:34850121
pmcid:PMC8728300
fatcat:w4ochry6hreqhjcqkaezuperpe
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