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Abstract

The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). This resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas.

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Figures

Figure 1
Figure 1
FANTOM5 assay flow and the data archive. Sample collection and data processing are indicated in a schematic view (green boxes). The resulting data and the analysis are collected into corresponding directories in the data archive (orange). GO, gene ontology.
Figure 2
Figure 2
Interfaces to FANTOM analyses. Scope and contents of the database systems.
Figure 3
Figure 3
Access to the sample details. Detailed information of a sample, including regulatory information produced by computational analysis of its transcriptome, is summarized in a page (dotted box on the left). This page can be found by examining pages of listed samples or tissue cell types, or by looking at (dis)similarities of samples in a transcriptome space defined by expression clustering (right boxes).
Figure 4
Figure 4
Inspection of a transcription factor and its activity. Detailed information on the most active CAGE peak at the SPI1 promoter is summarized in one page (dotted box, bottom left). This page can be found by examining the SPI1 gene on ZENBU (top left panel) or SSTAR (top right panel).
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References

    1. Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, et al. Functional annotation of a full-length mouse cDNA collection. Nature. 2001;409:685–690. doi: 10.1038/35055500. - DOI - PubMed
    1. Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420:563–573. doi: 10.1038/nature01266. - DOI - PubMed
    1. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, et al. The transcriptional landscape of the mammalian genome. Science 2005, 309:1559–1563. - PubMed
    1. NCBI. Resource Coordinators Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2013;41:D8–D20. doi: 10.1093/nar/gks1189. - DOI - PMC - PubMed
    1. Soejima H, Kawamoto S, Akai J, Miyoshi O, Arai Y, Morohka T, et al. Isolation of novel heart-specific genes using the BodyMap database. Genomics. 2001;74:115–120. doi: 10.1006/geno.2001.6527. - DOI - PubMed

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