TY - JOUR
T1 - Plant Reactome
T2 - A resource for plant pathways and comparative analysis
AU - Naithani, Sushma
AU - Preece, Justin
AU - D'Eustachio, Peter
AU - Gupta, Parul
AU - Amarasinghe, Vindhya
AU - Dharmawardhana, Palitha D.
AU - Wu, Guanming
AU - Fabregat, Antonio
AU - Elser, Justin L.
AU - Weiser, Joel
AU - Keays, Maria
AU - Fuentes, Alfonso Munoz Pomer
AU - Petryszak, Robert
AU - Stein, Lincoln D.
AU - Ware, Doreen
AU - Jaiswal, Pankaj
N1 - Publisher Copyright:
© The Author(s) 2016.
PY - 2017/1/1
Y1 - 2017/1/1
N2 - 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.
AB - 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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U2 - 10.1093/nar/gkw932
DO - 10.1093/nar/gkw932
M3 - Article
C2 - 27799469
AN - SCOPUS:85015991202
SN - 0305-1048
VL - 45
SP - D1029-D1039
JO - Nucleic acids research
JF - Nucleic acids research
IS - D1
ER -