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Updated: Jun 6, 2025

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
Published on: August 15, 2019
Update of the FANTOM web resource: enhancement for studying noncoding genomes
Tomoe Nobusada1, Chi Wai Yip1, Saumya Agrawal1
1RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Abstract:
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.
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