RARGE II: an integrated phenotype database of Arabidopsis mutant traits using a controlled vocabulary

Plant Cell Physiol. 2014 Jan;55(1):e4. doi: 10.1093/pcp/pct165. Epub 2013 Nov 21.


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.

Keywords: Arabidopsis; Database; Gene function; Mutant line; Ontology; Phenotype.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / anatomy & histology*
  • Arabidopsis / genetics*
  • Databases, Genetic*
  • Gene Ontology
  • Genes, Plant
  • Internet
  • Molecular Sequence Annotation
  • Mutation / genetics*
  • Phenotype
  • Quantitative Trait, Heritable*
  • User-Computer Interface
  • Vocabulary, Controlled*