RiceXPro Version 3.0: Expanding the informatics resource for rice transcriptome

Yutaka Sato, Hinako Takehisa, Kaori Kamatsuki, Hiroshi Minami, Nobukazu Namiki, Hiroshi Ikawa, Hajime Ohyanagi, Kazuhiko Sugimoto, Baltazar A. Antonio*, Yoshiaki Nagamura

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

170 Scopus citations

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.

Original languageEnglish (US)
JournalNucleic acids research
Volume41
Issue numberD1
DOIs
StatePublished - Jan 1 2013

ASJC Scopus subject areas

  • Genetics

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