Gateways to the FANTOM5 promoter level mammalian expression atlas
Open accessAbstract
The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource ( http://fantom.gsc.riken.jp/5/ ). This resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas.
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CAGE assays help the model relate TSS usage and strength to RNA-seq coverage between multiple alternative TSSs.
“which we reasoned would help the model relate TSS usage and strength to RNA-seq coverage between multiple (alternative) TSSs97,98”
From Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation (2025) · cites this paper as [98]
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Self-citationAn atlas of active enhancers across human cell types and tissues
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Self-citationGenome-wide analysis of mammalian promoter architecture and evolution
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“To classify samples systematically, we assembled the FANTOM Five (FF) Sample Ontology [23] consisting of the existing basic ontologies: cell types (CL), anatomical systems (UBERON), and diseases (DOID) [30-32].”
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“experiments, and protocols, we employed the MAGE/ ISA-tab file format [38,39], a standard format to describe”
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“Mining of CAGE-seq data to define CTS (cell-type specific), CTE (cell-type enriched), and UBQ (ubiquitous) TFs CAGE-seq data from FANTOM5 (Lizio et al , 2015) were used to define CTS, CTE and UBQ TF-encoding genes based on their patterns of expression in primary human and mouse cells.”
- Authors
- Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S., Mungall, C. J., Arner, E., Baillie, J. K., Bertin, N., Bono, H., de Hoon, M., Diehl, A. D., Dimont, E., Freeman, T. C., Fujieda, K., Hide, W., Kaliyaperumal, R., Katayama, T., Lassmann, T., Meehan, T. F., Nishikata, K., Ono, H., Rehli, M., Sandelin, A., Schultes, E. A., ‘t Hoen, P. A., Tatum, Z., Thompson, M., Toyoda, T., Wright, D. W., Daub, C. O., Itoh, M., Carninci, P., Hayashizaki, Y., Forrest, A. R., Kawaji, H., & the FANTOM consortium
- Affiliations
- RIKEN (JP)
- Roslin Institute (GB)
- National University of Singapore (SG)
- Research Organization of Information and Systems (JP)
- University at Buffalo, State University of New York (US)
- Harvard University (US)
- Leiden University Medical Center (NL)
- The Kids Research Institute Australia (AU)
- European Bioinformatics Institute (GB)
- University Hospital Regensburg (DE)
- University of Copenhagen (DK)
- Leiden University (NL)
- Corresponding author
- Forrest, Alistair RR
- Kawaji, Hideya
- ORCID
- Lizio, Marina
- Harshbarger, Jayson
- Severin, Jessica
- Kasukawa, Takeya
- Abugessaisa, Imad
- Baillie, J Kenneth
- Bertin, Nicolas
- Bono, Hidemasa
- Diehl, Alexander D
- Freeman, Tom C
- Kaliyaperumal, Rajaram
- Lassmann, Timo
- Meehan, Terrence F
- Ono, Hiromasa
- Rehli, Michael
- Sandelin, Albin
- Schultes, Erik A
- Tatum, Zuotian
- Daub, Carsten O
- Itoh, Masayoshi
- Carninci, Piero
- Hayashizaki, Yoshihide
- Forrest, Alistair RR
- Kawaji, Hideya
- Venue
- Genome Biology
- Published
- 2015-01-05
- Volume
- 16
- Issue
- 1
- Pages
- 22-22
- ISSN
- 1465-6906 (ISSN-L)
- PMC
- PMC4310165
- OpenAlex
- W2108797218
- Cited by
- 871
- References
- 11
- Citations by year
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- FWCI
- 28.96
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- UWA Profiles and Research Repository (UWA) (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- University of Regensburg Publication Server (University of Regensburg) (acceptedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, public-domain)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- Funders
- U.S. Department of Energy (-AC02-05CH11231, 05CH11231, DE AC02 05CH11231, DE-AC02-)
- John Templeton Foundation
- Wellcome Trust (103258/Z/13/Z)
- European Commission (305444, 2007–2013, FP7 2007-2013, DE-AC02-05CH11231, FP7/2007, 115191)
- Ministry of Education, Culture, Sports, Science and Technology (DE-AC02-05CH11231)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (FP7 2007-2013)
- Lundbeckfonden (R82-2010-6779)
- Novo Nordisk
- Novo Nordisk Fonden (NNF10SA1016550)
- H. Lundbeck A/S
- National Institutes of Health (R24OD011883)
- Directorate for Biological Sciences
- Office of Science (DEAC02–05CH11231, AC02-05CH11231, DE-AC02, 05CH11231)
- Biotechnology and Biological Sciences Research Council (BB/JO1446X/1, BBS/E/D/20241866, BBS/E/D/20241864, BB/F003722/1, BBS/E/D/20241863, BB/I001107/1)
- RIKEN
- Basic Energy Sciences (DE-AC02, DE-AC02-05CH11231., AC02–05CH11231)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- FANTOM5, promoter activity, transcription initiation, CAGE, data resources, transcription factors, enhancers
- MeSH terms
- Animals, Humans, Promoter Regions, Genetic, Software, User-Computer Interface, Computational Biology, Gene Expression Profiling, Genomics, Databases, Genetic, Mice, Transcriptome, Transcription Initiation, Genetic, Datasets as Topic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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