title: A web-based platform for rice microarray annotation and data analysis.
abstract: 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.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China.
authors.forename: Dijun
authors.initials: D
authors.lastname: Chen
authors.forename: Fan
authors.initials: F
authors.lastname: Zhang
authors.forename: Chunhui
authors.initials: C
authors.lastname: Yuan
authors.forename: Jing
authors.initials: J
authors.lastname: Lu
authors.forename: Xia
authors.initials: X
authors.lastname: Li
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface