Cargando…

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

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest fully public repository for high-throughput molecular abundance data, primarily gene expression data. The database has a flexible and open design that allows the submission, storage and retri...

Descripción completa

Detalles Bibliográficos
Autores principales: Barrett, Tanya, Suzek, Tugba O., Troup, Dennis B., Wilhite, Stephen E., Ngau, Wing-Chi, Ledoux, Pierre, Rudnev, Dmitry, Lash, Alex E., Fujibuchi, Wataru, Edgar, Ron
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539976/
https://www.ncbi.nlm.nih.gov/pubmed/15608262
http://dx.doi.org/10.1093/nar/gki022
_version_ 1782122094776025088
author Barrett, Tanya
Suzek, Tugba O.
Troup, Dennis B.
Wilhite, Stephen E.
Ngau, Wing-Chi
Ledoux, Pierre
Rudnev, Dmitry
Lash, Alex E.
Fujibuchi, Wataru
Edgar, Ron
author_facet Barrett, Tanya
Suzek, Tugba O.
Troup, Dennis B.
Wilhite, Stephen E.
Ngau, Wing-Chi
Ledoux, Pierre
Rudnev, Dmitry
Lash, Alex E.
Fujibuchi, Wataru
Edgar, Ron
author_sort Barrett, Tanya
collection PubMed
description The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest fully public repository for high-throughput molecular abundance data, primarily gene expression data. The database has a flexible and open design that allows the submission, storage and retrieval of many data types. These data include microarray-based experiments measuring the abundance of mRNA, genomic DNA and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. GEO currently holds over 30 000 submissions representing approximately half a billion individual molecular abundance measurements, for over 100 organisms. Here, we describe recent database developments that facilitate effective mining and visualization of these data. Features are provided to examine data from both experiment- and gene-centric perspectives using user-friendly Web-based interfaces accessible to those without computational or microarray-related analytical expertise. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.
format Text
id pubmed-539976
institution National Center for Biotechnology Information
language English
publishDate 2005
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-5399762005-01-04 NCBI GEO: mining millions of expression profiles—database and tools Barrett, Tanya Suzek, Tugba O. Troup, Dennis B. Wilhite, Stephen E. Ngau, Wing-Chi Ledoux, Pierre Rudnev, Dmitry Lash, Alex E. Fujibuchi, Wataru Edgar, Ron Nucleic Acids Res Articles The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the largest fully public repository for high-throughput molecular abundance data, primarily gene expression data. The database has a flexible and open design that allows the submission, storage and retrieval of many data types. These data include microarray-based experiments measuring the abundance of mRNA, genomic DNA and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. GEO currently holds over 30 000 submissions representing approximately half a billion individual molecular abundance measurements, for over 100 organisms. Here, we describe recent database developments that facilitate effective mining and visualization of these data. Features are provided to examine data from both experiment- and gene-centric perspectives using user-friendly Web-based interfaces accessible to those without computational or microarray-related analytical expertise. The GEO database is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo. Oxford University Press 2005-01-01 2004-12-17 /pmc/articles/PMC539976/ /pubmed/15608262 http://dx.doi.org/10.1093/nar/gki022 Text en Copyright © 2005 Oxford University Press
spellingShingle Articles
Barrett, Tanya
Suzek, Tugba O.
Troup, Dennis B.
Wilhite, Stephen E.
Ngau, Wing-Chi
Ledoux, Pierre
Rudnev, Dmitry
Lash, Alex E.
Fujibuchi, Wataru
Edgar, Ron
NCBI GEO: mining millions of expression profiles—database and tools
title NCBI GEO: mining millions of expression profiles—database and tools
title_full NCBI GEO: mining millions of expression profiles—database and tools
title_fullStr NCBI GEO: mining millions of expression profiles—database and tools
title_full_unstemmed NCBI GEO: mining millions of expression profiles—database and tools
title_short NCBI GEO: mining millions of expression profiles—database and tools
title_sort ncbi geo: mining millions of expression profiles—database and tools
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539976/
https://www.ncbi.nlm.nih.gov/pubmed/15608262
http://dx.doi.org/10.1093/nar/gki022
work_keys_str_mv AT barretttanya ncbigeominingmillionsofexpressionprofilesdatabaseandtools
AT suzektugbao ncbigeominingmillionsofexpressionprofilesdatabaseandtools
AT troupdennisb ncbigeominingmillionsofexpressionprofilesdatabaseandtools
AT wilhitestephene ncbigeominingmillionsofexpressionprofilesdatabaseandtools
AT ngauwingchi ncbigeominingmillionsofexpressionprofilesdatabaseandtools
AT ledouxpierre ncbigeominingmillionsofexpressionprofilesdatabaseandtools
AT rudnevdmitry ncbigeominingmillionsofexpressionprofilesdatabaseandtools
AT lashalexe ncbigeominingmillionsofexpressionprofilesdatabaseandtools
AT fujibuchiwataru ncbigeominingmillionsofexpressionprofilesdatabaseandtools
AT edgarron ncbigeominingmillionsofexpressionprofilesdatabaseandtools