RiceDB:基于Web界面的水稻基因芯片注释整合数据库

RiceDB:a Web-Based Integrated Database for Annotating Rice Microarray

开发了1个基于Web界面在生物学背景下注释水稻基因芯片的整合数据库RiceDB,它的注释信息比同类针对水稻Affymetrix 57K全基因组表达谱芯片的注释数据库更全面、更快捷且可以自动更新。它由8个功能模块组成,RiceMap建立水稻Affymetrix 57K探针组与基因的对应关系,从而提供来自各个水稻生物信息学数据库功能描述信息;RiceGO整合Gene Ontology数据库从生物学途径/分子功能和细胞构建对Affymetrix 57K探针组进行注释;RiceKO确定Affymetrix 57K探针组代表的基因可能参与的代谢与调控路径;RiceUP、RiceDO、RiceMR、RiceCD、RiceGF分别确定Affymetrix 57K探针组代表的基因上游小于1 kb启动子序列、结构功能域组成、受哪些水稻MicroRNA调控、染色体定位、基因家族分类。

Abstract： RiceDB, a web-based integrated database to annotate rice microarray in various biological contexts was developed. It provides convenient query for comprehensive and auto-updated annotation compared with other similar databases. It is composed of eight modules. RiceMap module archives the process of Affymetrix 57K probe sets mapping to different databases about rice, and aims to the genes represented by a microarray set by retrieving annotation information via identifier or accession number of every database; RiceGO module indicates the association between a microarray set and gene ontology categories consisting of biological process, molecular function and cellular component; RiceKO module is used to annotate a microarray set based on the KEGG biochemical and regulatory 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 is used to annotate the genes represented by a microarray set in the context of chromosome distribution; RiceGF is used to annotate the genes represented by a microarray set in the context of rice paralogous gene family distribution.