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RARTF specifications


Unique identifier OMICS_00562
Alternative name RIKEN Arabidopsis Transcription Factor database
Restrictions to use Academic or non-commercial use
Maintained Yes

Publication for RIKEN Arabidopsis Transcription Factor database

RARTF citations


An organ boundary enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation

Mol Syst Biol
PMCID: 4299377
PMID: 25358340
DOI: 10.15252/msb.20145470

[…] witz (). The cytokinin-responsive gene list was updated to include more comprehensive results from a recent study (Bhargava et al, ). TF classification was based on databases of AGRIS, PlantTFDB, and RARTF (Iida et al, ; Palaniswamy et al, ; Guo et al, ). Lists of TFs and hormone-responsive genes are available in Supplementary Tables S6 and S7. The gene enrichment analysis was quantified by log od […]


Functional Identification and Characterization of the Brassica Napus Transcription Factor Gene BnAP2, the Ortholog of Arabidopsis Thaliana APETALA2

PLoS One
PMCID: 3314020
PMID: 22479468
DOI: 10.1371/journal.pone.0033890

[…] To detect BnAP2 homolog in A. thaliana, all the protein sequences of AP2-domain genes in A. thaliana were downloaded from RARTF database (http://rarge.psc.riken.jp/rartf/) . Selected 145 Arabidopsis AP2-domain genes and target BnAP2 were used to constructed phylogenetic trees with the MEGA5.0 software package –. Phylogen […]


In Silico Analysis of Transcription Factor Repertoires and Prediction of Stress Responsive Transcription Factors from Six Major Gramineae Plants

PMCID: 3190953
PMID: 21729923
DOI: 10.1093/dnares/dsr019

[…] CBI BLAST program, as well as cross-reference links to different plant TF databases, including the general PlantTFDB and PlnTFDB, the grass-specific GRASSIUS, and the species-specific DATF, DRTF, and RARTF,–,– making it a comprehensive integrated database for comparative studies of the TFs derived from different plant species.Integration of expression analysis, cis-motif, and GO annotations as wel […]


A Central Regulatory System Largely Controls Transcriptional Activation and Repression Responses to Phosphate Starvation in Arabidopsis

PLoS Genet
PMCID: 2936532
PMID: 20838596
DOI: 10.1371/journal.pgen.1001102

[…] tor.com) . The two-fold up- and down-regulated genes were identified by the Meta-Analyser tool included in this platform. Transcription factor genes for transcriptomic analysis were identified in the RARTF Database (http://rarge.psc.riken.jp/rartf/) . […]


In silico Analysis of Transcription Factor Repertoire and Prediction of Stress Responsive Transcription Factors in Soybean

PMCID: 2780956
PMID: 19884168
DOI: 10.1093/dnares/dsp023

[…] nnotated GOs of TAIR8. Particular emphasis was placed on sequences serving under the ‘biological process’ functional category.TFs have been widely reported in plant TF databases such as DATF, AtTFDB, RARTF and PlnTFDB for Arabidopsis and DRTF, GRASIUS and PlnTFDB for rice. To annotate all putative soybean TFs in relation to Arabidopsis and rice counterparts, soybean TF sequences were assigned to a […]


Unbiased characterization of genotype dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana

BMC Syst Biol
PMCID: 2233643
PMID: 18028551
DOI: 10.1186/1752-0509-1-53

[…] ions.For a coexpression analysis of the transcription factor and coexpressed enzyme-coding gene pairs across the reactions for each metabolite, a list of 1968 transcription-factor genes was made from RIKEN Arabidopsis Transcription Factor database (RARTF) []. Using AGI code numbers in the list, coexpression analysis was performed using the tool "Correlated Gene Search" from the website []. The org […]


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RARTF institution(s)
Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Japan

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