Cargando…

NCBI GEO: mining tens of millions of expression profiles—database and tools update

The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. The database has a minimum information about a microarray experiment (MI...

Descripción completa

Detalles Bibliográficos
Autores principales: Barrett, Tanya, Troup, Dennis B., Wilhite, Stephen E., Ledoux, Pierre, Rudnev, Dmitry, Evangelista, Carlos, Kim, Irene F., Soboleva, Alexandra, Tomashevsky, Maxim, Edgar, Ron
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669752/
https://www.ncbi.nlm.nih.gov/pubmed/17099226
http://dx.doi.org/10.1093/nar/gkl887
_version_ 1782131123014336512
author Barrett, Tanya
Troup, Dennis B.
Wilhite, Stephen E.
Ledoux, Pierre
Rudnev, Dmitry
Evangelista, Carlos
Kim, Irene F.
Soboleva, Alexandra
Tomashevsky, Maxim
Edgar, Ron
author_facet Barrett, Tanya
Troup, Dennis B.
Wilhite, Stephen E.
Ledoux, Pierre
Rudnev, Dmitry
Evangelista, Carlos
Kim, Irene F.
Soboleva, Alexandra
Tomashevsky, Maxim
Edgar, Ron
author_sort Barrett, Tanya
collection PubMed
description The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. The database has a minimum information about a microarray experiment (MIAME)-compliant infrastructure that captures fully annotated raw and processed data. Several data deposit options and formats are supported, including web forms, spreadsheets, XML and Simple Omnibus Format in Text (SOFT). In addition to data storage, a collection of user-friendly web-based interfaces and applications are available to help users effectively explore, visualize and download the thousands of experiments and tens of millions of gene expression patterns stored in GEO. This paper provides a summary of the GEO database structure and user facilities, and describes recent enhancements to database design, performance, submission format options, data query and retrieval utilities. GEO is accessible at
format Text
id pubmed-1669752
institution National Center for Biotechnology Information
language English
publishDate 2007
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-16697522007-02-22 NCBI GEO: mining tens of millions of expression profiles—database and tools update Barrett, Tanya Troup, Dennis B. Wilhite, Stephen E. Ledoux, Pierre Rudnev, Dmitry Evangelista, Carlos Kim, Irene F. Soboleva, Alexandra Tomashevsky, Maxim Edgar, Ron Nucleic Acids Res Articles The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information (NCBI) archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. The database has a minimum information about a microarray experiment (MIAME)-compliant infrastructure that captures fully annotated raw and processed data. Several data deposit options and formats are supported, including web forms, spreadsheets, XML and Simple Omnibus Format in Text (SOFT). In addition to data storage, a collection of user-friendly web-based interfaces and applications are available to help users effectively explore, visualize and download the thousands of experiments and tens of millions of gene expression patterns stored in GEO. This paper provides a summary of the GEO database structure and user facilities, and describes recent enhancements to database design, performance, submission format options, data query and retrieval utilities. GEO is accessible at Oxford University Press 2007-01 2006-11-11 /pmc/articles/PMC1669752/ /pubmed/17099226 http://dx.doi.org/10.1093/nar/gkl887 Text en Published by Oxford University Press 2006 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) 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
Rudnev, Dmitry
Evangelista, Carlos
Kim, Irene F.
Soboleva, Alexandra
Tomashevsky, Maxim
Edgar, Ron
NCBI GEO: mining tens of millions of expression profiles—database and tools update
title NCBI GEO: mining tens of millions of expression profiles—database and tools update
title_full NCBI GEO: mining tens of millions of expression profiles—database and tools update
title_fullStr NCBI GEO: mining tens of millions of expression profiles—database and tools update
title_full_unstemmed NCBI GEO: mining tens of millions of expression profiles—database and tools update
title_short NCBI GEO: mining tens of millions of expression profiles—database and tools update
title_sort ncbi geo: mining tens of millions of expression profiles—database and tools update
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669752/
https://www.ncbi.nlm.nih.gov/pubmed/17099226
http://dx.doi.org/10.1093/nar/gkl887
work_keys_str_mv AT barretttanya ncbigeominingtensofmillionsofexpressionprofilesdatabaseandtoolsupdate
AT troupdennisb ncbigeominingtensofmillionsofexpressionprofilesdatabaseandtoolsupdate
AT wilhitestephene ncbigeominingtensofmillionsofexpressionprofilesdatabaseandtoolsupdate
AT ledouxpierre ncbigeominingtensofmillionsofexpressionprofilesdatabaseandtoolsupdate
AT rudnevdmitry ncbigeominingtensofmillionsofexpressionprofilesdatabaseandtoolsupdate
AT evangelistacarlos ncbigeominingtensofmillionsofexpressionprofilesdatabaseandtoolsupdate
AT kimirenef ncbigeominingtensofmillionsofexpressionprofilesdatabaseandtoolsupdate
AT sobolevaalexandra ncbigeominingtensofmillionsofexpressionprofilesdatabaseandtoolsupdate
AT tomashevskymaxim ncbigeominingtensofmillionsofexpressionprofilesdatabaseandtoolsupdate
AT edgarron ncbigeominingtensofmillionsofexpressionprofilesdatabaseandtoolsupdate