Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 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

Hiromasa Ono  1 , Osamu Ogasawara  2 , Kosaku Okubo  1   2 , Hidemasa Bono  1
Affiliations

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

Hiromasa Ono et al. Sci Data. .

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/.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing financial interests.

Figures

Figure 1
Figure 1. RefEx web interface.
This summary page shows the search results for liver-specific genes by clicking the liver icon at the top of the RefEx page (http://refex.dbcls.jp/).
Figure 2
Figure 2. Comparison view.
Up to three genes can be compared simultaneously. Users can compare all detailed information in parallel. The expression data and the overlapped annotated terms from Gene Ontology and the InterPro gene family are arranged in the same row.
Figure 3
Figure 3. FANTOM5/CAGE data viewer.
By clicking on the tab on the right-hand side, users can switch to a FANTOM5 CAGE data viewer. This viewer shows the expression patterns of all samples from the FANTOM5 CAGE data in the lower portion of the screen and displays an enlarged view of a specific area in the upper portion of the screen.
Figure 4
Figure 4. Comparison of human liver-specific genes obtained using different quantification methods for gene expression.
A Venn diagram of the human liver-specific genes in the GeneChip data and the RNA-Seq data. The Venn diagram was generated using the ‘Draw Venn Diagram’ website at http://bioinformatics.psb.ugent.be/webtools/Venn/.
See this image and copyright information in PMC

References

Data Citations

    1. Ono H. 2017. figshare. https://doi.org/10.6084/m9.figshare.c.3812815 - DOI
    1. Ono H. 2017. figshare. http://doi.org/10.6084/m9.figshare.4028685 - DOI
    1. Ono H. 2017. figshare. http://doi.org/10.6084/m9.figshare.4028688 - DOI
    1. 2017. NCBI Sequence Read Archive. ERP000546
    1. 2017. NCBI Sequence Read Archive. SRP000198

References

    1. Okubo K. et al. Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. Nat Genet. 2, 173–179 (1992). - PubMed
    1. Ogasawara O. et al. BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression. Nucleic Acids Res. 34, D628–D631 (2006). - PMC - PubMed
    1. Miki R. et al. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc Natl Acad Sci USA 98, 2199–2204 (2001). - PMC - PubMed
    1. Bono H. et al. RIKEN GER Group. GSL Members. Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res. 13, 1318–1323 (2003). - PMC - PubMed
    1. Bono H., Kasukawa T., Hayashizaki Y. & Okazak I. Y. READ: RIKEN Expression Array Database. Nucleic Acids Res. 30, 211–213 (2002). - PMC - PubMed

Publication types

LinkOut - more resources