OsCAS: A Web-based Comprehensive Annotation System For Rice Gene Chips

Rice (Oryza sativa) is one of the three major dietary staple foods in the world and has a highly synthetic genomic and gene structure with respect to other two major foods, maize (Zea mays) and wheat (Triticum aestivum). Two sub-species of rice, Oryza sativa japonica and Oryza sativa indica have been full-genome sequenced through the international cooperation leaded by IRGSP in 2002.Microarray technology is powerful in the investigation of a variety of crucial functional genomics questions including detecting the genes expressed in a given sample or genes differentially expressed between samples, classifying genes based on the expression profiles over time, etc. Along with the progress of microarray technology, the challenging issue becomes focused on how to analyze large amount of microarray data and make biological sense of them. Constructing a comprehensive, species-specific and systems biological platform to store, retrieve and predict relevant annotation information is meaningful. It can efficiently reduce the time and efforts spent on comparing data of multiple arrays and interpreting the possible biological implications associated with the gene expression differences.OsCAS(Oryza sativa Chips Annotation System) is a comprehensive web-based system to annotate the results of rice microarray experiments and analyze the relationship between genes based on their expression. This platform is designed to facilitate the study of differentially expressed genes within the framework of systems biological research. Through a user-friendly web interface, OsCAS accepts genechip probe IDs as inputs to retrieve relevant information by user-specified programs. In this system, public databases, including GenBank, UniGene, Swiss-Prot, TIGR, KOME, KEGG, Gene Ontology and miRBase were integrated to cover gene information, protein features, metabolic pathways and regulatory factors in rice. Apart from the available rice genomic information, OsCAS also involves the reprocessed information from several useful analytical tools such as CSRDB and miRU to guide a deep mining of the primary microarray annotation. OsCAS has been successfullyapplied in annotating large sets of genechip probe IDs from several rice microarrayexperiments and greatly facilitated the further analysis of differentially expressedgenes.