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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.  ...  INTRODUCTION The ArrayExpress Archive of Functional Genomics Data is one of the major international repositories for functional genomics high-throughput data.  ... 
doi:10.1093/nar/gkq1040 pmid:21071405 pmcid:PMC3013660 fatcat:4rn24k5lvzhajj4huiufljvsgy

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  ...  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.  ...  between ArrayExpress and ENA.  ... 
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  ...  The number of experiments based on sequencing technologies, in particular RNA-seq experiments, has been increasing over the last few years and submissions of sequencing data have overtaken microarray experiments  ...  INTRODUCTION ArrayExpress is an archive of functional genomics data that includes a range of experiment types, such as gene expression, methylation profiling and chromatin immunoprecipitation assays.  ... 
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.  ...  It stores functional genomics data derived from high throughput sequencing (HTS) and microarray-based experiments.  ... 
doi:10.1093/nar/gks1174 pmid:23193272 pmcid:PMC3531147 fatcat:un6k6u4xqfdjpjt6yhdg5lf6de

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  ...  The majority of the data are array based, but other data types are included, most recentlyultra high-throughput sequencing transcriptomics and epigenetic data.  ...  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

DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data

Yuichi Kodama, Jun Mashima, Takehide Kosuge, Osamu Ogasawara
2018 Nucleic Acids Research  
The Genomic Expression Archive (GEA) for functional genomics data from microarray and high-throughput sequencing experiments has been established at the DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp  ...  The DDBJ Center collects nucleotide sequence data and associated biological information from researchers and also services the Japanese Genotype-phenotype Archive (JGA) with the National Bioscience Database  ...  We are thankful to Minae Kawashima, Licht Toyo-oka and Nobutaka Mitsuhashi of the NBDC as collaborators of the JGA project; Takatomo Fujisawa for validator development; Eli Kaminuma for the DDBJ Read Annotation  ... 
doi:10.1093/nar/gky1002 pmid:30357349 pmcid:PMC6323915 fatcat:3bgfc6a3lvf6fjavejrvwixzne

The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments

Y. Kodama, J. Mashima, E. Kaminuma, T. Gojobori, O. Ogasawara, T. Takagi, K. Okubo, Y. Nakamura
2011 Nucleic Acids Research  
DOR is an archival database of functional genomics data generated by microarray and highly parallel new generation sequencers.  ...  The central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of all members of DDBJ for data collection, annotation and release and for software development.  ... 
doi:10.1093/nar/gkr994 pmid:22110025 pmcid:PMC3244990 fatcat:kbjrao6jw5hnrc4tcpq767mgsi

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  ...  extended to accept sequencing-based data.  ...  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

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  
EMBL, the European Commission grants: TEMBLOR, FELICS and MUGEN support ArrayExpress Development.  ...  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  ...  INTRODUCTION ArrayExpress (1) is a public database for storing and providing access to high throughput functional genomics data.  ... 
doi:10.1093/nar/gkl995 pmid:17132828 pmcid:PMC1716725 fatcat:yrtu55lvzzci5j57beyijo2hhe

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.  ...  treatments and other biological/ experimental conditions.  ...  and Nikolay Kolesnikov for help with ArrayExpress Archive interface.  ... 
doi:10.1093/nar/gkr913 pmid:22064864 pmcid:PMC3245177 fatcat:qi4tj2jmszh3zdkwmbwotggyo4

NCBI GEO: archive for functional genomics data sets—update

Tanya Barrett, Stephen E. Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F. Kim, Maxim Tomashevsky, Kimberly A. Marshall, Katherine H. Phillippy, Patti M. Sherman, Michelle Holko, Andrey Yefanov, Hyeseung Lee (+5 others)
2012 Nucleic Acids Research  
The Gene Expression Omnibus (GEO, http://www. ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted  ...  This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.  ...  INTRODUCTION The Gene Expression Omnibus (GEO) repository (1) archives and freely distributes microarray, next-generation sequencing (NGS) and other forms of high-throughput functional genomic data.  ... 
doi:10.1093/nar/gks1193 pmid:23193258 pmcid:PMC3531084 fatcat:cgkfwr2dlnepfo7si63m45tgeu

NCBI GEO: archive for functional genomics data sets--10 years on

T. Barrett, D. B. Troup, S. E. Wilhite, P. Ledoux, C. Evangelista, I. F. Kim, M. Tomashevsky, K. A. Marshall, K. H. Phillippy, P. M. Sherman, R. N. Muertter, M. Holko (+3 others)
2010 Nucleic Acids Research  
Today, GEO stores over 20 000 microarray-and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community.  ...  The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology.  ...  CONCLUSIONS Over the past decade, NCBI's GEO database has served as the major public archive for high-throughput microarrayand sequence-based functional genomic data sets.  ... 
doi:10.1093/nar/gkq1184 pmid:21097893 pmcid:PMC3013736 fatcat:gw3lqr47cbe3deubfht5nkaocu

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  
In parallel, high-throughput omics techniques had allowed picturing a larger spectrum of the behavior and characteristics of molecules in cancer and a large set of omics web-based tools and informative  ...  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

DDBJ progress report

E. Kaminuma, T. Kosuge, Y. Kodama, H. Aono, J. Mashima, T. Gojobori, H. Sugawara, O. Ogasawara, T. Takagi, K. Okubo, Y. Nakamura
2010 Nucleic Acids Research  
The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms.  ...  Moreover, we improved the content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based  ...  of database maintenance and INSD collaboration.  ... 
doi:10.1093/nar/gkq1041 pmid:21062814 pmcid:PMC3013661 fatcat:hqwqikzxbrhpvgsfc5fkecfzsy

All of gene expression (AOE): An integrated index for public gene expression databases

Hidemasa Bono, Robert Hoehndorf
2020 PLoS ONE  
Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE).  ...  These databases are useful resources for the functional interpretation of genes, but have been separately maintained and may lack RNA-seq data, while the original sequence data are available in the Sequence  ...  Yuichi Kodama for helpful advice for the integration of the DDBJ Genomic Expression Archive (GEA), and Dr. Takeru Nakazato and Dr.  ... 
doi:10.1371/journal.pone.0227076 pmid:31978081 fatcat:jm6wt3mn5fbvjiga4w4twy6tba
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