ArticlePlant & cell physiology2014
RARGE II: an integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary.
Article in Plant & cell physiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- Striking convergent selection history of wheat and barley and its potential for breeding.Nature plants · 2025Article
- Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences.Database : the journal of biological databases and curation · 2023Review
- Identification of growth regulators using cross-species network analysis in plants.Plant physiology · 2022Article
- A common language: Cross-species network analysis reveals growth regulators.Plant physiology · 2022Article
- R2R3-MYBs in Durum Wheat: Genome-Wide Identification, Poaceae-Specific Clusters, Expression, and Regulatory Dynamics Under Abiotic Stresses.Frontiers in plant science · 2022Article
- Metabolization and sequestration of plant specialized metabolites in insect herbivores: Current and emerging approaches.Frontiers in physiology · 2022Review
- Non-CG DNA methylation-deficiency mutations enhance mutagenesis rates during salt adaptation in cultured Arabidopsis cells.Stress biology · 2021Article
- Genome Evolutionary Dynamics Meets Functional Genomics: A Case Story on the Identification of SLC25A44.International journal of molecular sciences · 2021Article
- Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators.Nature plants · 2021Article
- A multilayered cross-species analysis of GRAS transcription factors uncovered their functional networks in plant adaptation to the environment.Journal of advanced research · 2021Article
- Proxies of CRISPR/Cas9 Activity To Aid in the Identification of Mutagenized Arabidopsis Plants.G3 (Bethesda, Md.) · 2020Article
- Comparative transcriptomics enables the identification of functional orthologous genes involved in early leaf growth.Plant biotechnology journal · 2020Article
- Identification of QTLs for Domestication-Related Traits in Zombi Pea [Frontiers in genetics · 2020Article
- Candidate Domestication-Related Genes Revealed by Expression Quantitative Trait Loci Mapping of Narrow-Leafed Lupin (International journal of molecular sciences · 2019Article
- Computational aspects underlying genome to phenome analysis in plants.The Plant journal : for cell and molecular biology · 2019Review
- Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes.Plant & cell physiology · 2017Article
- In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae.International journal of molecular sciences · 2015Article
- MOROKOSHI: transcriptome database in Sorghum bicolor.Plant & cell physiology · 2015Article
- Plant-PrAS: a database of physicochemical and structural properties and novel functional regions in plant proteomes.Plant & cell physiology · 2015Article
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6 authors.
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Abstract
Arabidopsis thaliana is one of the most popular experimental plants. However, only 40% of its genes have at least one experimental Gene Ontology (GO) annotation assigned. Systematic observation of mutant phenotypes is an important technique for elucidating gene functions. Indeed, several large-scale phenotypic analyses have been performed and have generated phenotypic data sets from many Arabidopsis mutant lines and overexpressing lines, which are freely available online. Since each Arabidopsis mutant line database uses individual phenotype expression, the differences in the structured term sets used by each database make it difficult to compare data sets and make it impossible to search across databases. Therefore, we obtained publicly available information for a total of 66,209 Arabidopsis mutant lines, including loss-of-function (RATM and TARAPPER) and gain-of-function (AtFOX and OsFOX) lines, and integrated the phenotype data by mapping the descriptions onto Plant Ontology (PO) and Phenotypic Quality Ontology (PATO) terms. This approach made it possible to manage the four different phenotype databases as one large data set. Here, we report a publicly accessible web-based database, the RIKEN Arabidopsis Genome Encyclopedia II (RARGE II; http://rarge-v2.psc.riken.jp/), in which all of the data described in this study are included. Using the database, we demonstrated consistency (in terms of protein function) with a previous study and identified the presumed function of an unknown gene. We provide examples of AT1G21600, which is a subunit in the plastid-encoded RNA polymerase complex, and AT5G56980, which is related to the jasmonic acid signaling pathway.
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