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RiceFREND specifications


Unique identifier OMICS_03282
Name RiceFREND
Restrictions to use None
Maintained Yes


  • Plants and Fungi
    • Oryza sativa


  • person_outline RiceXPro Team

Publication for RiceFREND

RiceFREND citations


Transcriptomic Analysis of Responses to Imbalanced Carbon: Nitrogen Availabilities in Rice Seedlings

PLoS One
PMCID: 5098742
PMID: 27820840
DOI: 10.1371/journal.pone.0165732
call_split See protocol

[…] iological process, cellular component and molecular function) of defined terms to describe the gene product attributes. High C:low N up-regulated genes were chosen to perform coexpression analysis by RiceFREND online web tool []. Functional analysis of the coexpression genes was performed using the KEGG pathway database (www.genome.jp/kegg/pathway.html). […]


Comprehensive Genomic Analysis and Expression Profiling of the NOX Gene Families under Abiotic Stresses and Hormones in Plants

Genome Biol Evol
PMCID: 4824067
PMID: 26907500
DOI: 10.1093/gbe/evw035
call_split See protocol

[…] of NOX genes in Arabidopsis and rice were performed using Mutual Rank (MR) values calculated by using the online tools ATTED-II (version 7.1, http://atted.jp/, last accessed February 29, 2016; ) and RiceFREND (version 2.0, http://ricefrend.dna.affrc.go.jp/, last accessed February 29, 2016; coexpression databases, respectively. The following criteria for interactome frameworks were performed at t […]


Action of multiple intra QTL genes concerted around a co localized transcription factor underpins a large effect QTL

Sci Rep
PMCID: 4623671
PMID: 26507552
DOI: 10.1038/srep15183

[…] first pass based on the number of SNPs in these analyses. After a literature survey and in silico analyses for gene ontology (GO; medcomp.medicina.unipd.it/Argot2/index.php), co-expression partners (RiceFREND: http://ricefrend.dna.affrc.go.jp/), promoter cis-regulatory elements (PLACE: http://www.dna.affrc.go.jp/PLACE/ and PlantCARE: http://bioinformatics.psb.ugent.be/webtools/plantcare/html/), p […]


'PP2C7s', Genes Most Highly Elaborated in Photosynthetic Organisms, Reveal the Bacterial Origin and Stepwise Evolution of PPM/PP2C Protein Phosphatases

PLoS One
PMCID: 4524716
PMID: 26241330
DOI: 10.1371/journal.pone.0132863

[…] C7 genes from [], and from RiceXPro ([]; http://ricexpro.dna.affrc.go.jp/). Plant gene co-expression network data for Arabidopsis were accessed at ATTED-II ([], []; http://atted.jp/), and for rice at RiceFREND ([]; http://ricefrend.dna.affrc.go.jp/). Arabidopsis promoter element analysis was performed using the tools within ATTED-II. Diurnal gene expression data for Arabidopsis was accessed at the […]


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RiceFREND institution(s)
Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan

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