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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. ...
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
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 ...
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
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 ...
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
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. ...
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
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 ...
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
2018
Nucleic Acids Research
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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
2011
Nucleic Acids Research
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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
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 ...
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
2007
Nucleic Acids Research
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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
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. ...
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
2012
Nucleic Acids Research
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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
2010
Nucleic Acids Research
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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
2020
Cancers of the Head & Neck
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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
2010
Nucleic Acids Research
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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
2020
PLoS ONE
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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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