Abstract
Gene expression data are exponentially accumulating; thus, the functional annotation of such sequence data from metadata is urgently required. However, life scientists have difficulty utilizing the available data due to its sheer magnitude and complicated access. We have developed a web tool for browsing reference gene expression pattern of mammalian tissues and cell lines measured using different methods, which should facilitate the reuse of the precious data archived in several public databases. The web tool is called Reference Expression dataset (RefEx), and RefEx allows users to search by the gene name, various types of IDs, chromosomal regions in genetic maps, gene family based on InterPro, gene expression patterns, or biological categories based on Gene Ontology. RefEx also provides information about genes with tissue-specific expression, and the relative gene expression values are shown as choropleth maps on 3D human body images from BodyParts3D. Combined with the newly incorporated Functional Annotation of Mammals (FANTOM) dataset, RefEx provides insight regarding the functional interpretation of unfamiliar genes. RefEx is publicly available at http://refex.dbcls.jp/.
Highlights
Profiling gene expression of tissues is important for the study of gene function
We have developed a web tool for browsing reference gene expression, which provides access to curated data from several other public databases, with expression levels in forty tissues measured by four well-established gene-expression quantification technologies
The web interface allows users to browse the expression profiles by the gene name, various types of IDs, chromosomal regions in genetic maps, gene family based on InterPro[11], gene expression patterns, or biological categories based on Gene Ontology[12]
Summary
Profiling gene expression of tissues is important for the study of gene function. Clues to gene function can often be obtained by examining when and where a gene is expressed in the tissues and cell lines. The gene expression patterns in various tissues and cell lines obtained by different quantification methods are helpful to properly infer the functions of unfamiliar genes in conjunction with available functional annotation of genes. The first attempt was to measure expression by counting the number of expressed sequence tags (ESTs) sequenced by traditional Sanger methods in different tissues[1,2]. After the invention of microarray, it was soon used for tissue profiling in the Functional Annotation of Mammals (FANTOM) project[3,4,5]. A similar effort for Affymetrix GeneChip microarrays was made by the BioGPS group[6]
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