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FANTOM5 CAGE specifications


Unique identifier OMICS_20496
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Content license CC Attribution
Maintained Yes


  • person_outline Michiel de Hoon
  • person_outline Alistair Forrest

Publication for FANTOM5 CAGE

FANTOM5 CAGE citations


Single cell full length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

Nat Commun
PMCID: 5809388
PMID: 29434199
DOI: 10.1038/s41467-018-02866-0

[…] For the analysis of enhancer RNA, we used genome mapping data (as described above).The permissive set of mouse enhancers identified using FANTOM5 CAGE data was downloaded from the FANTOM website ( The genomic coordinates of the enhancer annotation were converted from mm9 to […]


Linking FANTOM5 CAGE peaks to annotations with CAGEscan

Sci Data
PMCID: 5625555
PMID: 28972578
DOI: 10.1038/sdata.2017.147

[…] TOM5 core promoter atlas as seed, we clustered the CAGEscan paired-end reads in a collection of 112,315 models called CAGEscan clusters, by collating all the pairs whose alignment started in the same FANTOM5 CAGE peak. To de-orphanise FANTOM5 promoters, we intersected the CAGEscan clusters with GENCODE 18 gene models. Of the 85 % that intersected, 33,632 clusters had no annotation in FANTOM5, thus […]


Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture

Nucleic Acids Res
PMCID: 5737680
PMID: 28973462
DOI: 10.1093/nar/gkx680

[…] body regions (i.e. not representing first exons) were required to pass the histone mark filtering step, as described below for de novo identified candidate TSS.To identify TSS at 1-bp resolution, the FANTOM5 CAGE-seq datasets for each cell type were downloaded from the ftp resource ( in .bam format and converted into bedGraph signal files visual […]


Nanopore long read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

Nat Commun
PMCID: 5524981
PMID: 28722025
DOI: 10.1038/ncomms16027

[…] and quantify complex, never before observed, isoforms. Using ONT RNAseq on only seven B1a cells, we identified thousands of unannotated transcription start and end sites which we then validated using FANTOM5 CAGE data and polyA signals, respectively. Furthermore, we identified 696 genes displaying alternative transcription start and end site usage, and 354 genes with alternative splicing events. A […]


GTSE1: a novel TEAD4 E2F1 target gene involved in cell protrusions formation in triple negative breast cancer cell models

PMCID: 5620183
PMID: 28978043
DOI: 10.18632/oncotarget.18691

[…] 637, p-value < 2.2e-16), in order to have a stronger support to our analyses we decided to use for the subsequent steps all the breast cancer samples data (n=1100).The genomic regions surrounding the FANTOM5 CAGE peaks associated with the GTSE1 gene were analyzed using the ExPlain 3.1 suite (, MATCH tool) for the presence of transcription factor binding s […]


Transposon‐driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution

PMCID: 5494522
PMID: 28500258
DOI: 10.15252/embr.201744059

[…] onservation analysis, exons of the longest isoform of each transcript were matched to PhyloP scores for the mouse genome (UCSC). To assess the quality of TSS annotation, the assembly was compared to FANTOM5 CAGE peaks . Bedtools was used to identify the closest peak to the TSS of transcripts from coding and non‐coding clusters. These distances were compared to those of Ensembl transcripts. To ass […]

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FANTOM5 CAGE institution(s)
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan; Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, the Netherlands; [etc.]

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