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Plant Reactome: a resource for plant pathways and comparative analysis

Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome an...

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Autores principales: Naithani, Sushma, Preece, Justin, D'Eustachio, Peter, Gupta, Parul, Amarasinghe, Vindhya, Dharmawardhana, Palitha D., Wu, Guanming, Fabregat, Antonio, Elser, Justin L., Weiser, Joel, Keays, Maria, Fuentes, Alfonso Munoz-Pomer, Petryszak, Robert, Stein, Lincoln D., Ware, Doreen, Jaiswal, Pankaj
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210633/
https://www.ncbi.nlm.nih.gov/pubmed/27799469
http://dx.doi.org/10.1093/nar/gkw932
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author Naithani, Sushma
Preece, Justin
D'Eustachio, Peter
Gupta, Parul
Amarasinghe, Vindhya
Dharmawardhana, Palitha D.
Wu, Guanming
Fabregat, Antonio
Elser, Justin L.
Weiser, Joel
Keays, Maria
Fuentes, Alfonso Munoz-Pomer
Petryszak, Robert
Stein, Lincoln D.
Ware, Doreen
Jaiswal, Pankaj
author_facet Naithani, Sushma
Preece, Justin
D'Eustachio, Peter
Gupta, Parul
Amarasinghe, Vindhya
Dharmawardhana, Palitha D.
Wu, Guanming
Fabregat, Antonio
Elser, Justin L.
Weiser, Joel
Keays, Maria
Fuentes, Alfonso Munoz-Pomer
Petryszak, Robert
Stein, Lincoln D.
Ware, Doreen
Jaiswal, Pankaj
author_sort Naithani, Sushma
collection PubMed
description Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX.
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spelling pubmed-52106332017-01-05 Plant Reactome: a resource for plant pathways and comparative analysis Naithani, Sushma Preece, Justin D'Eustachio, Peter Gupta, Parul Amarasinghe, Vindhya Dharmawardhana, Palitha D. Wu, Guanming Fabregat, Antonio Elser, Justin L. Weiser, Joel Keays, Maria Fuentes, Alfonso Munoz-Pomer Petryszak, Robert Stein, Lincoln D. Ware, Doreen Jaiswal, Pankaj Nucleic Acids Res Database Issue Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX. Oxford University Press 2017-01-04 2016-10-30 /pmc/articles/PMC5210633/ /pubmed/27799469 http://dx.doi.org/10.1093/nar/gkw932 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Issue
Naithani, Sushma
Preece, Justin
D'Eustachio, Peter
Gupta, Parul
Amarasinghe, Vindhya
Dharmawardhana, Palitha D.
Wu, Guanming
Fabregat, Antonio
Elser, Justin L.
Weiser, Joel
Keays, Maria
Fuentes, Alfonso Munoz-Pomer
Petryszak, Robert
Stein, Lincoln D.
Ware, Doreen
Jaiswal, Pankaj
Plant Reactome: a resource for plant pathways and comparative analysis
title Plant Reactome: a resource for plant pathways and comparative analysis
title_full Plant Reactome: a resource for plant pathways and comparative analysis
title_fullStr Plant Reactome: a resource for plant pathways and comparative analysis
title_full_unstemmed Plant Reactome: a resource for plant pathways and comparative analysis
title_short Plant Reactome: a resource for plant pathways and comparative analysis
title_sort plant reactome: a resource for plant pathways and comparative analysis
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210633/
https://www.ncbi.nlm.nih.gov/pubmed/27799469
http://dx.doi.org/10.1093/nar/gkw932
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