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PLEXdb: gene expression resources for plants and plant pathogens

PLEXdb (http://www.plexdb.org), in partnership with community databases, supports comparisons of gene expression across multiple plant and pathogen species, promoting individuals and/or consortia to upload genome-scale data sets to contrast them to previously archived data. These analyses facilitate...

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Detalles Bibliográficos
Autores principales: Dash, Sudhansu, Van Hemert, John, Hong, Lu, Wise, Roger P., Dickerson, Julie A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245067/
https://www.ncbi.nlm.nih.gov/pubmed/22084198
http://dx.doi.org/10.1093/nar/gkr938
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author Dash, Sudhansu
Van Hemert, John
Hong, Lu
Wise, Roger P.
Dickerson, Julie A.
author_facet Dash, Sudhansu
Van Hemert, John
Hong, Lu
Wise, Roger P.
Dickerson, Julie A.
author_sort Dash, Sudhansu
collection PubMed
description PLEXdb (http://www.plexdb.org), in partnership with community databases, supports comparisons of gene expression across multiple plant and pathogen species, promoting individuals and/or consortia to upload genome-scale data sets to contrast them to previously archived data. These analyses facilitate the interpretation of structure, function and regulation of genes in economically important plants. A list of Gene Atlas experiments highlights data sets that give responses across different developmental stages, conditions and tissues. Tools at PLEXdb allow users to perform complex analyses quickly and easily. The Model Genome Interrogator (MGI) tool supports mapping gene lists onto corresponding genes from model plant organisms, including rice and Arabidopsis. MGI predicts homologies, displays gene structures and supporting information for annotated genes and full-length cDNAs. The gene list-processing wizard guides users through PLEXdb functions for creating, analyzing, annotating and managing gene lists. Users can upload their own lists or create them from the output of PLEXdb tools, and then apply diverse higher level analyses, such as ANOVA and clustering. PLEXdb also provides methods for users to track how gene expression changes across many different experiments using the Gene OscilloScope. This tool can identify interesting expression patterns, such as up-regulation under diverse conditions or checking any gene’s suitability as a steady-state control.
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spelling pubmed-32450672012-01-10 PLEXdb: gene expression resources for plants and plant pathogens Dash, Sudhansu Van Hemert, John Hong, Lu Wise, Roger P. Dickerson, Julie A. Nucleic Acids Res Articles PLEXdb (http://www.plexdb.org), in partnership with community databases, supports comparisons of gene expression across multiple plant and pathogen species, promoting individuals and/or consortia to upload genome-scale data sets to contrast them to previously archived data. These analyses facilitate the interpretation of structure, function and regulation of genes in economically important plants. A list of Gene Atlas experiments highlights data sets that give responses across different developmental stages, conditions and tissues. Tools at PLEXdb allow users to perform complex analyses quickly and easily. The Model Genome Interrogator (MGI) tool supports mapping gene lists onto corresponding genes from model plant organisms, including rice and Arabidopsis. MGI predicts homologies, displays gene structures and supporting information for annotated genes and full-length cDNAs. The gene list-processing wizard guides users through PLEXdb functions for creating, analyzing, annotating and managing gene lists. Users can upload their own lists or create them from the output of PLEXdb tools, and then apply diverse higher level analyses, such as ANOVA and clustering. PLEXdb also provides methods for users to track how gene expression changes across many different experiments using the Gene OscilloScope. This tool can identify interesting expression patterns, such as up-regulation under diverse conditions or checking any gene’s suitability as a steady-state control. Oxford University Press 2012-01 2011-11-14 /pmc/articles/PMC3245067/ /pubmed/22084198 http://dx.doi.org/10.1093/nar/gkr938 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Dash, Sudhansu
Van Hemert, John
Hong, Lu
Wise, Roger P.
Dickerson, Julie A.
PLEXdb: gene expression resources for plants and plant pathogens
title PLEXdb: gene expression resources for plants and plant pathogens
title_full PLEXdb: gene expression resources for plants and plant pathogens
title_fullStr PLEXdb: gene expression resources for plants and plant pathogens
title_full_unstemmed PLEXdb: gene expression resources for plants and plant pathogens
title_short PLEXdb: gene expression resources for plants and plant pathogens
title_sort plexdb: gene expression resources for plants and plant pathogens
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245067/
https://www.ncbi.nlm.nih.gov/pubmed/22084198
http://dx.doi.org/10.1093/nar/gkr938
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