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DatasetFANTOM
The FANTOM web resource describes functional annotations and tools for exploring mammalian noncoding genomes, including long noncoding RNA data.
About FANTOM
FANTOM is a web resource that provides functional annotations and tools for exploring mammalian noncoding genomes, with a focus on long noncoding RNAs (lncRNAs). Its 2025 update adds curated functional information for lncRNAs, including data from induced pluripotent stem (iPS) cells, and chromatin-interaction-based annotations of nuclear lncRNAs.
The site also hosts fanta.bio, which collects cis-regulatory elements (CREs) identified from transcriptional activity detected with CAGE and related methods. Each CRE region is annotated with activity levels, neighboring genes, and links to genetic variation and transcription factor binding resources. The homepage excerpt is largely a list of research updates and publications. It does not describe search, download, or access terms in detail.
Key features
- Curated functional annotations for long noncoding RNAs, including iPS cell data
- Chromatin-interaction-based annotations of nuclear long noncoding RNAs
- Catalog of transcriptionally active cis-regulatory elements
- CRE regions annotated with activity levels and neighboring genes
- Links to genetic variation and transcription factor binding resources
- Promoter and enhancer atlases extended with FANTOM6 CAGE profiles
Best for: Researchers studying transcriptional regulation and noncoding RNAs in mammalian genomes.
Good for
- Connects CRE activity data to neighboring genes and to genetic variation and transcription factor binding resources
- Identifies regions where transcripts are actively transcribed, rather than inferring elements from chromatin marks alone
- Updates are tied to published papers, with a DOI given for the 2025 update
FANTOM at a glance
- Official website
- fantom.gsc.riken.jp
- Category
- Research & Data › Open Data & Datasets
- Type
- Dataset
- Platforms
- Web
- Language
- English
- Country
- JP
- Last checked
- Oct 6, 2026 · Online when checked
- Listed
- Oct 5, 2026
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FANTOM FAQ
What does fanta.bio identify?
fanta.bio identifies genomic elements around which transcripts are actively transcribed, such as mRNA, lncRNA, eRNA, and uaRNA, using CAGE and related protocols.
Does the lncRNA annotation cover iPS cells?
Yes. The 2025 update adds curated functional information for long noncoding RNAs, including data from iPS cells.
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