RiceCyc statistics

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RiceCyc specifications

Information


Unique identifier OMICS_02772
Name RiceCyc
Restrictions to use None
Maintained Yes

Taxon


  • Plants and Fungi
    • Oryza sativa

Publication for RiceCyc

RiceCyc citations

 (9)
library_books

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

2018
PMCID: 5946812
PMID: 29762652
DOI: 10.1093/database/bay035

[…] /yeast.biocyc.org/), mammals [Bos taurus in CattleCyc ()] and plants such as Arabidopsis thaliana in AraCyc (, ), Medicago truncatula in MedicCyc (), Fragaria vesca in FragariaCyc (), Oryza sativa in RiceCyc () and Zea mays in MaizeCyc (). While most PGDBs are created at the species level, this is not required and they can be generated at arbitrary levels in the taxonomic hierarchy. For instance, […]

library_books

Crosstalk between diurnal rhythm and water stress reveals an altered primary carbon flux into soluble sugars in drought treated rice leaves

2017
Sci Rep
PMCID: 5557844
PMID: 28811563
DOI: 10.1038/s41598-017-08473-1

[…] we developed a functional interaction network mediated by 276 genes that encode the components of the entire starch biosynthesis and degradation pathways (Fig.¬†, Table¬†). These were derived from the RiceCyc Interaction Viewer (http://pathway.gramene.org/gramene/ricecyc.shtml) and the Rice Interaction Viewer (http://bar.utoronto.ca/interactions/cgi-bin/riceinteractionsviewer.cgi), . From this, we […]

library_books

Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement

2016
Front Plant Sci
PMCID: 5126141
PMID: 27965696
DOI: 10.3389/fpls.2016.01795

[…] c network which can be analyzed using structural metabolic modeling and constraint-based modeling techniques such as FBA. The statistics of rice GSMN/GEMs are summarized in Table .The two rice GSMNs, RiceCyc () and RiceGEM (), are accessible online as databases with information on genes, proteins and reactions. RiceCyc is a rice-specific metabolic pathway database constructed based on MetaCyc and […]

library_books

Functional classification of rice flanking sequence tagged genes using MapMan terms and global understanding on metabolic and regulatory pathways affected by dxr mutant having defects in light response

2016
PMCID: 4830809
PMID: 27076183
DOI: 10.1186/s12284-016-0089-2

[…] selected downstream pathways, accelerating the understanding of mechanisms and providing us with better options for application of the results. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and RiceCyc databases (http://pathway.gramene.org/gramene/ricecyc.shtml) also provide a catalog of known or predicted rice biochemical pathways (Dharmawardhana et al. ; Sakurai et al. ). […]

library_books

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

2013
PMCID: 4883713
PMID: 24280345
DOI: 10.1186/1939-8433-6-15

[…] The RiceCyc pathway database currently features 316 metabolic pathways, 2,103 enzymatic reactions, 87 transport reactions and 1,543 compounds and metabolites. 6,643 protein coding genes i.e. about 14% of […]

library_books

Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits

2012
Biotechnol Biofuels
PMCID: 3502489
PMID: 23122416
DOI: 10.1186/1754-6834-5-80

[…] . Gene function annotations include conserved protein domains (e.g. Interpro [], Gene Ontology (GO) terms [], and biochemical pathways (e.g. KEGG; []) including well annotated metabolic enzymes (e.g. RiceCyc at Gramene []). These annotation terms provide clues into what a gene near the biomarker is doing including possible pathway involvement, an indicator of gene-gene interaction and complex trai […]

Citations

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RiceCyc institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK; Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto, Canada; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA; NAA Plant, Soil & Nutrition Laboratory Research Unit, USDA-ARS, Ithaca, NY, USA

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