FANTOM Web Resource update 2025
This page serves as a supplementary landing page for Nobusada et al., "Update of the FANTOM Web Resource: Enhancement for Studying Noncoding Genomes" (2025). Below are highlights of the latest updates:
1. Functional annotation of lncRNAs in human iPS cells
To explore the potential functional roles of each lncRNA, we performed knockdown experiments on 390 lncRNAs and obtained their cellular phenotypes (e.g., growth rates) and molecular phenotypes (e.g., transcriptome profiles). We provide five interfaces for exploring these experimental and analytical results.
- Growth rates upon the lncRNA knockdowns by ASO
This interface shows changes in growth rates following the knockdown of each lncRNA. - Genomic properties of target genes
This interface displays the predicted subcellular localizations of target lncRNAs. - Differentially expressed genes upon the lncRNA knockdowns by ASO
This interface lists the differentially expressed genes resulting from the knockdown of each lncRNA. - Gene Set Enrichment Analysis (GSEA) upon the lncRNA knockdowns by ASO
This interface provides enriched networks and Gene Ontology (GO) terms for differentially expressed genes following lncRNA knockdown. - Motif Activity Response Analysis (MARA) upon the lncRNA knockdowns by ASO
This interface provides enriched transcription factor binding sites (TFBS) by comparing transcriptome profiles of knockdown and control samples.
2. Chromatin interaction for nuclear lncRNA functional annotation
To explore potential lncRNA functions, we analyzed the genomic interaction of lncRNAs to other genes with Hi-C data. We provide six interfaces to browse the analysis results of lncRNAs and their target genes.
- Comparison of lncRNA annotations among cell types
This interface provides annotations for lncRNAs based on target genes whose promoters are spatially close to lncRNA genes based on chromatin interactions identified using Hi-C data. The annotations include lncRNA expression levels across various cell lines, GO term annotations for lncRNA target genes (presented as heatmaps), enriched TFBSs in target genes, and enriched GWAS traits in A/B compartments containing lncRNA target genes. - Comparison of lncRNA Enrichr annotations
This interface displays enriched Enrichr gene sets within the target genes of a specified lncRNA. - LncRNA characterization report
This interface enables browsing of target genes of individual lncRNA in a selected cell type identified using Hi-C chromatin interaction. By selecting a gene, users can view a list of reference lncRNAs that target the gene. Selecting a reference lncRNA will display all candidate target genes and their network with the lncRNA and associated annotations. - Annotated interactions per gene
This interface provides a list and network visualization of genes connected via Hi-C interactions with specified genes. By selecting a gene, users can view a list of genes from different gene classes, including mRNA, lncRNA, and enhancers that interact with the selected genes. - Annotated differential Hi-C genomic interactions
This interface shows differentially interacting annotated chromatin regions between two selected cell lines. - LncRNAs associated with GO and Enrichr annotation categories
This interface allows users to search for lncRNAs associated with specific Gene Ontology terms or Enrichr gene sets.
3. Expansion of the transcribed CRE atlas – fanta.bio
In FANTOM5, we developed promoter and enhancer atlases in human and mouse using over 3,000 biological samples. To expand these atlases with new CAGE and CAGE-like profiles (e.g., NET-CAGE), we created a new database called fanta.bio.
4. Collaborative integration with external databases
- UCSC Genome Browser
The FANTOM5 track is integrated with native tracks. - The International Human Epigenome Consortium (IHEC) Data Portal
The FANTOM5 human dataset can be added to the IHEC data grid view by clicking the "[+Add External DataHub]" button at the bottom of the data grid. - ChIP-Atlas
The FANTOM5 enhancer dataset is included in the Annotation Track and can be compared with ChIP-Atlas peak data. - RIKEN MetaDatabase
Metadata from FANTOM5 datasets is stored in the RIKEN MetaDatabase and can be queried through their interface.