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ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression

H. Parkinson, M. Kapushesky, N. Kolesnikov, G. Rustici, M. Shojatalab, N. Abeygunawardena, H. Berube, M. Dylag, I. Emam, A. Farne, E. Holloway, M. Lukk (+22 others)
2009 Nucleic Acids Research  
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

Nikolay Kolesnikov, Emma Hastings, Maria Keays, Olga Melnichuk, Y. Amy Tang, Eleanor Williams, Miroslaw Dylag, Natalja Kurbatova, Marco Brandizi, Tony Burdett, Karyn Megy, Ekaterina Pilicheva (+6 others)
2014 Nucleic Acids Research  
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

Awais Athar, Anja Füllgrabe, Nancy George, Haider Iqbal, Laura Huerta, Ahmed Ali, Catherine Snow, Nuno A Fonseca, Robert Petryszak, Irene Papatheodorou, Ugis Sarkans, Alvis Brazma
2018 Nucleic Acids Research  
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

Gabriella Rustici, Nikolay Kolesnikov, Marco Brandizi, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Jon Ison, Maria Keays, Natalja Kurbatova, James Malone (+14 others)
2012 Nucleic Acids Research  
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

H. Parkinson, U. Sarkans, N. Kolesnikov, N. Abeygunawardena, T. Burdett, M. Dylag, I. Emam, A. Farne, E. Hastings, E. Holloway, N. Kurbatova, M. Lukk (+10 others)
2010 Nucleic Acids Research  
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

M. Kapushesky, T. Adamusiak, T. Burdett, A. Culhane, A. Farne, A. Filippov, E. Holloway, A. Klebanov, N. Kryvych, N. Kurbatova, P. Kurnosov, J. Malone (+10 others)
2011 Nucleic Acids Research  
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

Ugis Sarkans, Anja Füllgrabe, Ahmed Ali, Awais Athar, Ehsan Behrangi, Nestor Diaz, Silvie Fexova, Nancy George, Haider Iqbal, Sandeep Kurri, Jhoan Munoz, Juan Rada (+2 others)
2020 Nucleic Acids Research  
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

Irene Papatheodorou, Nuno A Fonseca, Maria Keays, Y Amy Tang, Elisabet Barrera, Wojciech Bazant, Melissa Burke, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Nancy George, Laura Huerta, Satu Koskinen (+10 others)
2017 Nucleic Acids Research  
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

Misha Kapushesky, Ibrahim Emam, Ele Holloway, Pavel Kurnosov, Andrey Zorin, James Malone, Gabriella Rustici, Eleanor Williams, Helen Parkinson, Alvis Brazma
2009 Nucleic Acids Research  
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

H. Parkinson, M. Kapushesky, M. Shojatalab, N. Abeygunawardena, R. Coulson, A. Farne, E. Holloway, N. Kolesnykov, P. Lilja, M. Lukk, R. Mani, T. Rayner (+4 others)
2007 Nucleic Acids Research  
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  
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

Robert Petryszak, Tony Burdett, Benedetto Fiorelli, Nuno A. Fonseca, Mar Gonzalez-Porta, Emma Hastings, Wolfgang Huber, Simon Jupp, Maria Keays, Nataliya Kryvych, Julie McMurry, John C. Marioni (+9 others)
2013 Nucleic Acids Research  
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

Mara S. Serafini, Laura Lopez-Perez, Giuseppe Fico, Lisa Licitra, Loris De Cecco, Carlo Resteghini
2020 Cancers of the Head & Neck  
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

Robert Petryszak, Maria Keays, Y. Amy Tang, Nuno A. Fonseca, Elisabet Barrera, Tony Burdett, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Simon Jupp, Satu Koskinen, Oliver Mannion, Laura Huerta (+12 others)
2015 Nucleic Acids Research  
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

Pablo Moreno, Silvie Fexova, Nancy George, Jonathan R Manning, Zhichiao Miao, Suhaib Mohammed, Alfonso Muñoz-Pomer, Anja Fullgrabe, Yalan Bi, Natassja Bush, Haider Iqbal, Upendra Kumbham (+22 others)
2021 Nucleic Acids Research  
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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