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BarleyBase—an expression profiling database for plant genomics
BarleyBase (BB) (www.barleybase.org) is an online database for plant microarrays with integrated tools for data visualization and statistical analysis. BB houses raw and normalized expression data from the two publicly available Affymetrix genome arrays, Barley1 and Arabidopsis ATH1 with plans to in...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2005
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540077/ https://www.ncbi.nlm.nih.gov/pubmed/15608273 http://dx.doi.org/10.1093/nar/gki123 |
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author | Shen, Lishuang Gong, Jian Caldo, Rico A. Nettleton, Dan Cook, Dianne Wise, Roger P. Dickerson, Julie A. |
author_facet | Shen, Lishuang Gong, Jian Caldo, Rico A. Nettleton, Dan Cook, Dianne Wise, Roger P. Dickerson, Julie A. |
author_sort | Shen, Lishuang |
collection | PubMed |
description | BarleyBase (BB) (www.barleybase.org) is an online database for plant microarrays with integrated tools for data visualization and statistical analysis. BB houses raw and normalized expression data from the two publicly available Affymetrix genome arrays, Barley1 and Arabidopsis ATH1 with plans to include the new Affymetrix 61K wheat, maize, soybean and rice arrays, as they become available. BB contains a broad set of query and display options at all data levels, ranging from experiments to individual hybridizations to probe sets down to individual probes. Users can perform cross-experiment queries on probe sets based on observed expression profiles and/or based on known biological information. Probe set queries are integrated with visualization and analysis tools such as the R statistical toolbox, data filters and a large variety of plot types. Controlled vocabularies for gene and plant ontologies, as well as interconnecting links to physical or genetic map and other genomic data in PlantGDB, Gramene and GrainGenes, allow users to perform EST alignments and gene function prediction using Barley1 exemplar sequences, thus, enhancing cross-species comparison. |
format | Text |
id | pubmed-540077 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2005 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-5400772005-01-04 BarleyBase—an expression profiling database for plant genomics Shen, Lishuang Gong, Jian Caldo, Rico A. Nettleton, Dan Cook, Dianne Wise, Roger P. Dickerson, Julie A. Nucleic Acids Res Articles BarleyBase (BB) (www.barleybase.org) is an online database for plant microarrays with integrated tools for data visualization and statistical analysis. BB houses raw and normalized expression data from the two publicly available Affymetrix genome arrays, Barley1 and Arabidopsis ATH1 with plans to include the new Affymetrix 61K wheat, maize, soybean and rice arrays, as they become available. BB contains a broad set of query and display options at all data levels, ranging from experiments to individual hybridizations to probe sets down to individual probes. Users can perform cross-experiment queries on probe sets based on observed expression profiles and/or based on known biological information. Probe set queries are integrated with visualization and analysis tools such as the R statistical toolbox, data filters and a large variety of plot types. Controlled vocabularies for gene and plant ontologies, as well as interconnecting links to physical or genetic map and other genomic data in PlantGDB, Gramene and GrainGenes, allow users to perform EST alignments and gene function prediction using Barley1 exemplar sequences, thus, enhancing cross-species comparison. Oxford University Press 2005-01-01 2004-12-17 /pmc/articles/PMC540077/ /pubmed/15608273 http://dx.doi.org/10.1093/nar/gki123 Text en Copyright © 2005 Oxford University Press |
spellingShingle | Articles Shen, Lishuang Gong, Jian Caldo, Rico A. Nettleton, Dan Cook, Dianne Wise, Roger P. Dickerson, Julie A. BarleyBase—an expression profiling database for plant genomics |
title | BarleyBase—an expression profiling database for plant genomics |
title_full | BarleyBase—an expression profiling database for plant genomics |
title_fullStr | BarleyBase—an expression profiling database for plant genomics |
title_full_unstemmed | BarleyBase—an expression profiling database for plant genomics |
title_short | BarleyBase—an expression profiling database for plant genomics |
title_sort | barleybase—an expression profiling database for plant genomics |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540077/ https://www.ncbi.nlm.nih.gov/pubmed/15608273 http://dx.doi.org/10.1093/nar/gki123 |
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