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

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the res...

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Autores principales: Barrett, Tanya, Troup, Dennis B., Wilhite, Stephen E., Ledoux, Pierre, Evangelista, Carlos, Kim, Irene F., Tomashevsky, Maxim, Marshall, Kimberly A., Phillippy, Katherine H., Sherman, Patti M., Muertter, Rolf N., Holko, Michelle, Ayanbule, Oluwabukunmi, Yefanov, Andrey, Soboleva, Alexandra
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013736/
https://www.ncbi.nlm.nih.gov/pubmed/21097893
http://dx.doi.org/10.1093/nar/gkq1184
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author Barrett, Tanya
Troup, Dennis B.
Wilhite, Stephen E.
Ledoux, Pierre
Evangelista, Carlos
Kim, Irene F.
Tomashevsky, Maxim
Marshall, Kimberly A.
Phillippy, Katherine H.
Sherman, Patti M.
Muertter, Rolf N.
Holko, Michelle
Ayanbule, Oluwabukunmi
Yefanov, Andrey
Soboleva, Alexandra
author_facet Barrett, Tanya
Troup, Dennis B.
Wilhite, Stephen E.
Ledoux, Pierre
Evangelista, Carlos
Kim, Irene F.
Tomashevsky, Maxim
Marshall, Kimberly A.
Phillippy, Katherine H.
Sherman, Patti M.
Muertter, Rolf N.
Holko, Michelle
Ayanbule, Oluwabukunmi
Yefanov, Andrey
Soboleva, Alexandra
author_sort Barrett, Tanya
collection PubMed
description A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. 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. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/.
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spelling pubmed-30137362011-01-03 NCBI GEO: archive for functional genomics data sets—10 years on Barrett, Tanya Troup, Dennis B. Wilhite, Stephen E. Ledoux, Pierre Evangelista, Carlos Kim, Irene F. Tomashevsky, Maxim Marshall, Kimberly A. Phillippy, Katherine H. Sherman, Patti M. Muertter, Rolf N. Holko, Michelle Ayanbule, Oluwabukunmi Yefanov, Andrey Soboleva, Alexandra Nucleic Acids Res Articles A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. 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. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/. Oxford University Press 2011-01 2010-11-20 /pmc/articles/PMC3013736/ /pubmed/21097893 http://dx.doi.org/10.1093/nar/gkq1184 Text en Published by Oxford University Press 2010. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Barrett, Tanya
Troup, Dennis B.
Wilhite, Stephen E.
Ledoux, Pierre
Evangelista, Carlos
Kim, Irene F.
Tomashevsky, Maxim
Marshall, Kimberly A.
Phillippy, Katherine H.
Sherman, Patti M.
Muertter, Rolf N.
Holko, Michelle
Ayanbule, Oluwabukunmi
Yefanov, Andrey
Soboleva, Alexandra
NCBI GEO: archive for functional genomics data sets—10 years on
title NCBI GEO: archive for functional genomics data sets—10 years on
title_full NCBI GEO: archive for functional genomics data sets—10 years on
title_fullStr NCBI GEO: archive for functional genomics data sets—10 years on
title_full_unstemmed NCBI GEO: archive for functional genomics data sets—10 years on
title_short NCBI GEO: archive for functional genomics data sets—10 years on
title_sort ncbi geo: archive for functional genomics data sets—10 years on
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013736/
https://www.ncbi.nlm.nih.gov/pubmed/21097893
http://dx.doi.org/10.1093/nar/gkq1184
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