Update of the FANTOM web resource: enhancement for studying noncoding genomes
The FANTOM web resource (https://fantom.gsc.riken.jp/) has been a unique resource for studying mammalian genomes, which is built on the research activities conducted in the international collaborative project FANTOM (Functional ANnoTation Of the Mammalian genome). In recent updates, we expanded annotations for long non-coding RNAs (lncRNAs) and transcribed cis-regulatory elements (CREs). The former was derived from the large-scale lncRNA perturbations in induced pluripotent stem cells (iPSCs) and integrative analysis of Hi-C data conducted in the sixth iteration of the project (FANTOM6). The resulting annotations of lncRNAs, according to the impact on cellular and molecular phenotypes and the potential RNA-chromatin interactions, are accessible via the interactive ZENBU-Reports framework. The latter involves a new platform, fanta.bio (https://fanta.bio/), which collects transcribed CREs identified via use of an extended dataset of CAGE profiles. The CREs, with their annotations including genetic and epigenetic information, are accessible via a dedicated interface as well as the UCSC Genome Browser Database. These updates offer enhanced opportunities to investigate the functions of non-coding regions within mammalian genomes.
Authors
- Chikashi C. Terao (ORCID: https://orcid.org/0000-0002-6452-4095)
- Kayoko Yasuzawa (ORCID: https://orcid.org/0000-0002-1362-3093)
- Toyoyuki Takada (ORCID: https://orcid.org/0000-0001-6796-2085)
- Jay W. Shin (ORCID: https://orcid.org/0000-0003-4037-3533)
- Atsushi Kondo (ORCID: https://orcid.org/0000-0002-1175-7485)
- Scott Walker
- Chung-Chau Hon (ORCID: https://orcid.org/0000-0002-3741-7577)
- Masaru Koido (ORCID: https://orcid.org/0000-0002-0348-0666)
- Michiel de Hoon (ORCID: https://orcid.org/0000-0003-0489-2352)
- Shinya Oki (ORCID: https://orcid.org/0000-0002-4767-3259)
- Imad Abugessaisa (ORCID: https://orcid.org/0000-0001-7458-801X)
- Hideya Kawaji (ORCID: https://orcid.org/0000-0002-0575-0308)
- Michihira Tagami (ORCID: https://orcid.org/0000-0002-9713-3576)
- Saumya Agrawal
- Hiroshi Masuya (ORCID: https://orcid.org/0000-0002-3392-466X)
- Takeya Kasukawa (ORCID: https://orcid.org/0000-0001-5085-0802)
- Soichiro Ide (ORCID: https://orcid.org/0000-0002-9112-2841)
- Piero Carninci (ORCID: https://orcid.org/0000-0001-7202-7243)
- Nishad Thalhath (ORCID: https://orcid.org/0000-0001-9845-9714)
- Chi Wai Yip (ORCID: https://orcid.org/0000-0003-3327-5695)
- Akira Hasegawa (ORCID: https://orcid.org/0000-0002-7674-6955)
- Jessica Severin
- Tomoe Nobusada (ORCID: https://orcid.org/0000-0002-4133-1565)
Institutions
- RIKEN BioResource Research Center (JP)
- Tokyo Metropolitan Institute of Medical Science (JP)
- Shizuoka General Hospital (JP)
- RIKEN Center for Integrative Medical Sciences (JP)
- The University of Tokyo (JP)
- Kumamoto University (JP)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2024-11-27
- DOI
- https://doi.org/10.1093/nar/gkae1047
- Citations
- 7
- Primary Topic
- Cancer-related molecular mechanisms research
- Type
- article
- Field-Weighted Citation Impact
- 2.00
Funders
- Japan Agency for Medical Research and Development
- Ministry of Education, Culture, Sports, Science and Technology
- RIKEN
- National Bioscience Database Center