ArticleScientific data2017
Linking FANTOM5 CAGE peaks to annotations with CAGEscan.
Article in Scientific data, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.
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Who cites it
14 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Sex-stratified genome-wide association meta-analysis of major depressive disorder.Nature communications · 2025Pooled it
- A transformer-based method for the cap analysis of gene expression and gene expression tag associated capping region prediction in RNA.RNA biology · 2026Article
- Gene-centered representation of coding and regulatory variation enables outcome prediction.bioRxiv : the preprint server for biology · 2026Article
- An improved method for the highly specific detection of transcription start sites.Nucleic acids research · 2024Article
- Atlas of primary cell-type-specific sequence models of gene expression and variant effects.Cell reports methods · 2023Article
- Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.G3 (Bethesda, Md.) · 2023Article
- A versatile 5' RACE-Seq methodology for the accurate identification of the 5' termini of mRNAs.BMC genomics · 2022Article
- TSSr: an R package for comprehensive analyses of TSS sequencing data.NAR genomics and bioinformatics · 2021Article
- Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer.Frontiers in genetics · 2021Review
- TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.Nucleic acids research · 2020Article
- Article
- Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Frontiers in genetics · 2020Article
- Update of the FANTOM web resource: expansion to provide additional transcriptome atlases.Nucleic acids research · 2019Article
- Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts.Computational and structural biotechnology journal · 2019Review
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Authors and funding
14 authors.
Funding
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Abstract
The FANTOM5 expression atlas is a quantitative measurement of the activity of nearly 200,000 promoter regions across nearly 2,000 different human primary cells, tissue types and cell lines. Generation of this atlas was made possible by the use of CAGE, an experimental approach to localise transcription start sites at single-nucleotide resolution by sequencing the 5' ends of capped RNAs after their conversion to cDNAs. While 50% of CAGE-defined promoter regions could be confidently associated to adjacent transcriptional units, nearly 100,000 promoter regions remained gene-orphan. To address this, we used the CAGEscan method, in which random-primed 5'-cDNAs are paired-end sequenced. Pairs starting in the same region are assembled in transcript models called CAGEscan clusters. Here, we present the production and quality control of CAGEscan libraries from 56 FANTOM5 RNA sources, which enhances the FANTOM5 expression atlas by providing experimental evidence associating core promoter regions with their cognate transcripts.
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