A web-based platform for rice microarray annotation and data analysis  

作　　者：CHEN DiJun ZHANG Fan YUAN ChunHui LU Jing LI Xia CHEN Ming 

机构地区：[1]College of Bioinformatics Science and Technology,Harbin Medical University,Harbin 150086,China [2]College of Life Science,Zhejiang University,Hangzhou 310058,China [3]Zhejiang California International Nanosystems Institute,Zhejiang University,Hangzhou 310058,China

出　　处：《Science China(Life Sciences)》2010年第12期1467-1473,共7页中国科学(生命科学英文版)

基　　金：supported by the National Natural Science Foundation of China (Grant Nos. 30600367 and 30771326);the National High-Tech Research and Development Program of China (Grant No. 2007AA02Z329);the National Basic Research Program of China (Grant Nos. 2007AA02Z329 and 2008AA10Z125);Heilongjiang Science & Technology Key Project (Grant No. 2008CB517302)

摘　　要：Rice(Oryza sativa) feeds over half of the global population.A web-based integrated platform for rice microarray annotation and data analysis in various biological contexts is presented,which provides a convenient query for comprehensive annotation compared with similar databases.Coupled with existing rice microarray data,it provides online analysis methods from the perspective of bioinformatics.This comprehensive bioinformatics analysis platform is composed of five modules,including data retrieval,microarray annotation,sequence analysis,results visualization and data analysis.The BioChip module facilitates the retrieval of microarray data information via identifiers of "Probe Set ID","Locus ID" and "Analysis Name".The BioAnno module is used to annotate the gene or probe set based on the gene function,the domain information,the KEGG biochemical and regulatory pathways and the potential microRNA which regulates the genes.The BioSeq module lists all of the related sequence information by a microarray probe set.The BioView module provides various visual results for the microarray data.The BioAnaly module is used to analyze the rice microarray's data set.Rice(Oryza sativa) feeds over half of the global population.A web-based integrated platform for rice microarray annotation and data analysis in various biological contexts is presented,which provides a convenient query for comprehensive annotation compared with similar databases.Coupled with existing rice microarray data,it provides online analysis methods from the perspective of bioinformatics.This comprehensive bioinformatics analysis platform is composed of five modules,including data retrieval,microarray annotation,sequence analysis,results visualization and data analysis.The BioChip module facilitates the retrieval of microarray data information via identifiers of "Probe Set ID","Locus ID" and "Analysis Name".The BioAnno module is used to annotate the gene or probe set based on the gene function,the domain information,the KEGG biochemical and regulatory pathways and the potential microRNA which regulates the genes.The BioSeq module lists all of the related sequence information by a microarray probe set.The BioView module provides various visual results for the microarray data.The BioAnaly module is used to analyze the rice microarray’s data set.

关 键 词：RICE MICROARRAY ANNOTATION data analysis 

分 类 号：S511[农业科学—作物学]