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RiceXPro：一个用于监测在自然田间条件下种植的粳稻基因表达的平台。

RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions.

作者信息

Sato Yutaka, Antonio Baltazar A, Namiki Nobukazu, Takehisa Hinako, Minami Hiroshi, Kamatsuki Kaori, Sugimoto Kazuhiko, Shimizu Yuji, Hirochika Hirohiko, Nagamura Yoshiaki

机构信息

Genome Resource Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.

出版信息

Nucleic Acids Res. 2011 Jan;39(Database issue):D1141-8. doi: 10.1093/nar/gkq1085. Epub 2010 Nov 2.

DOI:10.1093/nar/gkq1085
PMID:21045061
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3013682/
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.

摘要

阐明水稻中所有预测基因的功能仍是谷物基因组学的最终目标，以便确保培育出改良品种，从而养活不断增长的世界人口。我们构建了一个基因表达数据库（RiceXPro，网址：http://ricexpro.dna.affrc.go.jp/），以概述田间水稻植株整个生长过程中的转录变化。RiceXPro包含两个数据集，分别对应于各种器官和组织的时空基因表达谱，以及从移栽到收获期间叶片的连续基因表达谱。用户友好的网络界面可通过关键词和染色体搜索提取特定的基因表达谱，并进行基本数据分析，从而提供有关特定基因表达的器官/组织和发育阶段特异性的有用信息。诸如t检验、倍数变化计算和相关度计算等分析工具有助于比较两个随机样本之间的表达谱，并预测未表征基因的功能。作为一个涵盖田间生长的表达数据储存库，该数据库可以提供水稻各种重要农艺性状背后基因的基线信息。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f21a/3013682/89ebff73b39c/gkq1085f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f21a/3013682/55bc188a3cbb/gkq1085f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f21a/3013682/b96d511d975b/gkq1085f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f21a/3013682/2f896c7035e7/gkq1085f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f21a/3013682/89ebff73b39c/gkq1085f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f21a/3013682/55bc188a3cbb/gkq1085f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f21a/3013682/b96d511d975b/gkq1085f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f21a/3013682/2f896c7035e7/gkq1085f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f21a/3013682/89ebff73b39c/gkq1085f4.jpg

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