| RiceDB： A Web-Based Integrated Database for Annotating Rice Microarray |
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| 引用本文： | HE Fei SHI Qing-yun CHEN Ming WU Ping. RiceDB： A Web-Based Integrated Database for Annotating Rice Microarray[J]. 水稻科学, 2007, 14(4): 256-264 |
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| 作者姓名： | HE Fei SHI Qing-yun CHEN Ming WU Ping |
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| 作者单位： | State Key Laboratory of Plant Physiology ＆ Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 3100584 China |
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| 基金项目： | 国家重点基础研究发展计划(973计划);国家自然科学基金;国家教育部海外归国学者科研基金;浙江省科技厅资助项目 |
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| 摘 要： | RiceDB, a web-based integrated database to annotate rice microarray in various biological contexts was developed. It is composed of eight modules. RiceMap module archives the process of Affymetrix probe sets mapping to different databases about rice, and aims to the genes represented by a microarray set by retrieving annotation information via the identifier or accession number of every database; RiceGO module indicates the association between a microarray set and gene ontology (GO) categories; RiceKO module is used to annotate a microarray set based on the KEGG biochemical pathways; RiceDO module indicates the information of domain associated with a microarray set; RiceUP module is used to obtain promoter sequences for all genes represented by a microarray set; RiceMR module lists potential microRNA which regulated the genes represented by a microarray set; RiceCD and RiceGF are used to annotate the genes represented by a microarray set in the context of chromosome distribution and rice paralogous family distribution. The results of automatic annotation are mostly consistent with manual annotation. Biological interpretation of the microarray data is quickened by the help of RiceDB.
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| 关 键 词： | 分子数据库 综合管理 稻子 栽培技术 |
| 收稿时间： | 2007-05-08 |
| 修稿时间： | 2007-07-11 |
RiceDB: A Web-Based Integrated Database for Annotating Rice Microarray |
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| HE Fei,SHI Qing-yun,CHEN Ming,WU Ping. RiceDB: A Web-Based Integrated Database for Annotating Rice Microarray[J]. Rice science, 2007, 14(4): 256-264 |
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| Authors: | HE Fei SHI Qing-yun CHEN Ming WU Ping |
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| Affiliation: | State Key Laboratory of Plant Physiology & Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; # These authors contributed equally to this paper |
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| Abstract: | RiceDB, a web-based integrated database to annotate rice microarray in various biological contexts was developed. It is composed of eight modules. RiceMap module archives the process of Affymetrix probe sets mapping to different databases about rice, and aims to the genes represented by a microarray set by retrieving annotation information via the identifier or accession number of every database; RiceGO module indicates the association between a microarray set and gene ontology (GO) categories; RiceKO module is used to annotate a microarray set based on the KEGG biochemical pathways; RiceDO module indicates the information of domain associated with a microarray set; RiceUP module is used to obtain promoter sequences for all genes represented by a microarray set; RiceMR module lists potential microRNA which regulated the genes represented by a microarray set; RiceCD and RiceGF are used to annotate the genes represented by a microarray set in the context of chromosome distribution and rice paralogous family distribution. The results of automatic annotation are mostly consistent with manual annotation. Biological interpretation of the microarray data is quickened by the help of RiceDB. |
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| Keywords: | Affymetrix microarray annotation Oryza sativa molecular database |
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