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
. 2021 Jan 8;49(D1):D892-D898.
doi: 10.1093/nar/gkaa1054.

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

Imad Abugessaisa  1 , Jordan A Ramilowski  1   2 , Marina Lizio  1 , Jesicca Severin  1 , Akira Hasegawa  1 , Jayson Harshbarger  1 , Atsushi Kondo  1 , Shuhei Noguchi  1 , Chi Wai Yip  1 , Jasmine Li Ching Ooi  1 , Michihira Tagami  1 , Fumi Hori  1 , Saumya Agrawal  1 , Chung Chau Hon  1 , Melissa Cardon  1 , Shuya Ikeda  3 , Hiromasa Ono  3 , Hidemasa Bono  3   4 , Masaki Kato  1 , Kosuke Hashimoto  1 , Alessandro Bonetti  1   5 , Masaki Kato  6 , Norio Kobayashi  6 , Jay Shin  1 , Michiel de Hoon  1 , Yoshihide Hayashizaki  1 , Piero Carninci  1 , Hideya Kawaji  1   7   8 , Takeya Kasukawa  1   9
Affiliations

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

Imad Abugessaisa et al. Nucleic Acids Res. .

Abstract

The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Overview of FANTOM5 and FANTOM6 web resources: new and existing resources generated in FANTOM5 and FANTOM6 projects. The light-gray boxes show the atlas or dataset and the dark-gray boxes show the method used to generate them.
Figure 2.
Figure 2.
Access to the FANTOM6 data web resources: (A) web resources interface for FANTOM6 experiments in tabular view for each CAGE library with associated attributes; (B) web resource experiments view can be refined by the check-box and adjusted; (C and D) provide a list, files and a grid view, respectively, of selected experiments as in (B); (E) analysis results of FANTOM6 pilot project using ZENBU analysis report view.
Figure3.
Figure3.
Access to the miRNA atlas sample metadata and analysis results: (A) the list of chicken, rat and dog samples and their metadata are provided in FANTOM5 SSTAR resource; (B) ZENBU report for miRNA atlas allows for interactive browsing of miRNAs detected in given samples and for exploring their promoter(s) expression. The raw reads and alignments are available through the FANTOM5 data files repository.
See this image and copyright information in PMC

References

    1. Kawai J., Shinagawa A., Shibata K., Yoshino M., Itoh M., Ishii Y., Arakawa T., Hara A., Fukunishi Y., Konno H. et al. .. Functional annotation of a full-length mouse cDNA collection. Nature. 2001; 409:685–690. - PubMed
    1. de Hoon M., Shin J.W., Carninci P.. Paradigm shifts in genomics through the FANTOM projects. Mamm. Genome. 2015; 26:391–402. - PMC - PubMed
    1. Andersson R., Gebhard C., Miguel-Escalada I., Hoof I., Bornholdt J., Boyd M., Chen Y., Zhao X., Schmidl C., Suzuki T. et al. .. An atlas of active enhancers across human cell types and tissues. Nature. 2014; 507:455–461. - PMC - PubMed
    1. Forrest A.R., Kawaji H., Rehli M., Baillie J.K., de Hoon M.J., Haberle V., Lassmann T., Kulakovskiy I.V., Lizio M., Itoh M. et al. .. A promoter-level mammalian expression atlas. Nature. 2014; 507:462–470. - PMC - PubMed
    1. Arner E., Daub C.O., Vitting-Seerup K., Andersson R., Lilje B., Drabløs F., Lennartsson A., Rönnerblad M., Hrydziuszko O., Vitezic M. et al. .. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015; 347:1010–1014. - PMC - PubMed

Publication types