- RiceXPro version 3.0: expanding the informatics resource for rice transcriptome. [PMID: 23180765]
Yutaka Sato, Hinako Takehisa, Kaori Kamatsuki, Hiroshi Minami, Nobukazu Namiki, Hiroshi Ikawa, Hajime Ohyanagi, Kazuhiko Sugimoto, Baltazar A Antonio, Yoshiaki Nagamura
Nucleic acids research 2013:41(Database issue)
66 Citations (Google Scholar as of 2016-04-25)
Abstract: A wide range of resources on gene expression profiling enhance various strategies in plant molecular biology particularly in characterization of gene function. We have updated our gene expression profile database, RiceXPro (http://ricexpro.dna.affrc.go.jp/), to provide more comprehensive information on the transcriptome of rice encompassing the entire growth cycle and various experimental conditions. The gene expression profiles are currently grouped into three categories, namely, 'field/development' with 572 data corresponding to 12 data sets, 'plant hormone' with 143 data corresponding to 13 data sets and 'cell- and tissue-type' comprising of 38 microarray data. In addition to the interface for retrieving expression information of a gene/genes in each data set, we have incorporated an interface for a global approach in searching an overall view of the gene expression profiles from multiple data sets within each category. Furthermore, we have also added a BLAST search function that enables users to explore expression profile of a gene/genes with similarity to a query sequence. Therefore, the updated version of RiceXPro can be used more efficiently to survey the gene expression signature of rice in sufficient depth and may also provide clues on gene function of other cereal crops.
- RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions. [PMID: 21045061]
Yutaka Sato, Baltazar A Antonio, Nobukazu Namiki, Hinako Takehisa, Hiroshi Minami, Kaori Kamatsuki, Kazuhiko Sugimoto, Yuji Shimizu, Hirohiko Hirochika, Yoshiaki Nagamura
Nucleic acids research 2011:39(Database issue)
123 Citations (Google Scholar as of 2016-04-25)
Abstract: Elucidating the function of all predicted genes in rice remains as the ultimate goal in cereal genomics in order to ensure the development of improved varieties that will sustain an expanding world population. We constructed a gene expression database (RiceXPro, URL: http://ricexpro.dna.affrc.go.jp/) to provide an overview of the transcriptional changes throughout the growth of the rice plant in the field. RiceXPro contains two data sets corresponding to spatiotemporal gene expression profiles of various organs and tissues, and continuous gene expression profiles of leaf from transplanting to harvesting. A user-friendly web interface enables the extraction of specific gene expression profiles by keyword and chromosome search, and basic data analysis, thereby providing useful information as to the organ/tissue and developmental stage specificity of expression of a particular gene. Analysis tools such as t-test, calculation of fold change and degree of correlation facilitate the comparison of expression profiles between two random samples and the prediction of function of uncharacterized genes. As a repository of expression data encompassing growth in the field, this database can provide baseline information of genes that underlie various agronomically important traits in rice.