title: Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis.
abstract: Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au).
authors.affiliation: ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, MCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia; Centre for Computational Systems Biology, University of Western Australia, MCS Building M316, 35 Stirling Highway, Crawley, 6009, Western Australia, Australia.
authors.forename: Reena
authors.initials: R
authors.lastname: Narsai
authors.forename: James
authors.initials: J
authors.lastname: Devenish
authors.forename: Ian
authors.initials: I
authors.lastname: Castleden
authors.forename: Kabir
authors.initials: K
authors.lastname: Narsai
authors.forename: Lin
authors.initials: L
authors.lastname: Xu
authors.forename: Huixia
authors.initials: H
authors.lastname: Shou
authors.forename: James
authors.initials: J
authors.lastname: Whelan
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D005075:Biological Evolution; D030541:Databases, Genetic; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D020407:Internet; D008928:Mitochondria / Q000235:genetics; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D020543:Proteome; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D012984:Software; D059467:Transcriptome; D014584:User-Computer Interface
chemical_list: D010940:Plant Proteins; D020543:Proteome; D012333:RNA, Messenger; D018749:RNA, Plant
keywords: Arabidopsis; Arabidopsis thaliana; Oryza sativa; protein; rice; subcellular location; transcript expression