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Sci Data. 2017 Aug 29;4:170105. doi: 10.1038/sdata.2017.105.

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes.

Author information

1
Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 1111 Yata, Mishima 411-8540, Japan.
2
Center for Information Biology, National Institute of Genetics, Research Organization for Information and Systems, 1111 Yata, Mishima 411-8540, Japan.

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/.

PMID:
28850115
PMCID:
PMC5574374
DOI:
10.1038/sdata.2017.105
[Indexed for MEDLINE]
Free PMC Article

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