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Title: Gateways to the FANTOM5 promoter level mammalian expression atlas

Abstract

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/). In conclusion, 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.

Authors:
 [1];  [1];  [1];  [1];  [2];  [1];  [2];  [3];  [1];  [1];  [4];  [1];  [5];  [6];  [7];  [1];  [8];  [9];  [5];  [7] more »;  [10];  [11];  [7];  [12];  [13];  [14];  [7];  [15];  [16];  [17];  [11];  [11];  [11];  [14];  [5];  [3];  [18];  [1];  [19];  [1];  [20] « less
+ Show Author Affiliations
  1. RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan)
  2. RIKEN Center for Life Science Technologie, Kanagawa (Japan)
  3. RIKEN Yokohama Institute, Kanagawa (Japan)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. Univ. of Edinburgh, Scotland (United Kingdom)
  6. RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan); National Univ. of Singapore (Singapore)
  7. Research Organization of Information Systems, Chiba (Japan)
  8. Univ. at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY (United States)
  9. Harvard School of Public Health, Boston, MA (United States)
  10. Harvard School of Public Health, Boston, MA (United States); Univ. of Sheffield, Sheffield (United Kingdom)
  11. Leiden Univ. Medical Center, Leiden (Netherlands)
  12. RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan); The Univ. of Western Australia, Western Australia (Australia)
  13. European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge (United Kingdom)
  14. RIKEN Advanced Center for Computing and Communication, Saitama (Japan)
  15. Univ. Hospital Regensburg, Regensburg (Germany)
  16. Copenhagen Univ., Copenhagen (Denmark)
  17. Leiden Univ. Medical Center, Leiden (Netherlands); Leiden Univ., Leiden (Netherlands)
  18. RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan); RIKEN Preventive Medicine and Diagnosis Innovative Program, Saitama (Japan)
  19. RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Preventive Medicine and Diagnosis Innovative Program, Saitama (Japan)
  20. RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan); RIKEN Preventive Medicine and Diagnosis Innovative Program, Saitama (Japan); RIKEN Advanced Center for Computing and Communication, Saitama (Japan)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
Contributing Org.:
The FANTOM consortium
OSTI Identifier:
1256488
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
GenomeBiology.com
Additional Journal Information:
Journal Volume: 16; Journal Issue: 1; Journal ID: ISSN 1465-6906
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING

Citation Formats

Lizio, Marina, Harshbarger, Jayson, Shimoji, Hisashi, Severin, Jessica, Kasukawa, Takeya, Sahin, Serkan, Abugessaisa, Imad, Fukuda, Shiro, Hori, Fumi, Ishikawa-Kato, Sachi, Mungall, Christopher J., Arner, Erik, Baillie, J. Kenneth, Bertin, Nicolas, Bono, Hidemasa, de Hoon, Michiel, Diehl, Alexander D., Dimont, Emmanuel, Freeman, Tom C., Fujieda, Kaori, Hide, Winston, Kaliyaperumal, Rajaram, Katayama, Toshiaki, Lassmann, Timo, Meehan, Terrence F., Nishikata, Koro, Ono, Hiromasa, Rehli, Michael, Sandelin, Albin, Schultes, Erik A., ‘t Hoen, Peter A. C., Tatum, Zuotian, Thompson, Mark, Toyoda, Tetsuro, Wright, Derek W., Daub, Carsten O., Itoh, Masayoshi, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., and Kawaji, Hideya. Gateways to the FANTOM5 promoter level mammalian expression atlas. United States: N. p., 2015. Web. doi:10.1186/s13059-014-0560-6.
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Lizio, Marina, Harshbarger, Jayson, Shimoji, Hisashi, Severin, Jessica, Kasukawa, Takeya, Sahin, Serkan, Abugessaisa, Imad, Fukuda, Shiro, Hori, Fumi, Ishikawa-Kato, Sachi, Mungall, Christopher J., Arner, Erik, Baillie, J. Kenneth, Bertin, Nicolas, Bono, Hidemasa, de Hoon, Michiel, Diehl, Alexander D., Dimont, Emmanuel, Freeman, Tom C., Fujieda, Kaori, Hide, Winston, Kaliyaperumal, Rajaram, Katayama, Toshiaki, Lassmann, Timo, Meehan, Terrence F., Nishikata, Koro, Ono, Hiromasa, Rehli, Michael, Sandelin, Albin, Schultes, Erik A., ‘t Hoen, Peter A. C., Tatum, Zuotian, Thompson, Mark, Toyoda, Tetsuro, Wright, Derek W., Daub, Carsten O., Itoh, Masayoshi, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., & Kawaji, Hideya. Gateways to the FANTOM5 promoter level mammalian expression atlas. United States. https://doi.org/10.1186/s13059-014-0560-6
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Lizio, Marina, Harshbarger, Jayson, Shimoji, Hisashi, Severin, Jessica, Kasukawa, Takeya, Sahin, Serkan, Abugessaisa, Imad, Fukuda, Shiro, Hori, Fumi, Ishikawa-Kato, Sachi, Mungall, Christopher J., Arner, Erik, Baillie, J. Kenneth, Bertin, Nicolas, Bono, Hidemasa, de Hoon, Michiel, Diehl, Alexander D., Dimont, Emmanuel, Freeman, Tom C., Fujieda, Kaori, Hide, Winston, Kaliyaperumal, Rajaram, Katayama, Toshiaki, Lassmann, Timo, Meehan, Terrence F., Nishikata, Koro, Ono, Hiromasa, Rehli, Michael, Sandelin, Albin, Schultes, Erik A., ‘t Hoen, Peter A. C., Tatum, Zuotian, Thompson, Mark, Toyoda, Tetsuro, Wright, Derek W., Daub, Carsten O., Itoh, Masayoshi, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., and Kawaji, Hideya. Mon . "Gateways to the FANTOM5 promoter level mammalian expression atlas". United States. https://doi.org/10.1186/s13059-014-0560-6. https://www.osti.gov/servlets/purl/1256488.
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@article{osti_1256488,
title = {Gateways to the FANTOM5 promoter level mammalian expression atlas},
author = {Lizio, Marina and Harshbarger, Jayson and Shimoji, Hisashi and Severin, Jessica and Kasukawa, Takeya and Sahin, Serkan and Abugessaisa, Imad and Fukuda, Shiro and Hori, Fumi and Ishikawa-Kato, Sachi and Mungall, Christopher J. and Arner, Erik and Baillie, J. Kenneth and Bertin, Nicolas and Bono, Hidemasa and de Hoon, Michiel and Diehl, Alexander D. and Dimont, Emmanuel and Freeman, Tom C. and Fujieda, Kaori and Hide, Winston and Kaliyaperumal, Rajaram and Katayama, Toshiaki and Lassmann, Timo and Meehan, Terrence F. and Nishikata, Koro and Ono, Hiromasa and Rehli, Michael and Sandelin, Albin and Schultes, Erik A. and ‘t Hoen, Peter A. C. and Tatum, Zuotian and Thompson, Mark and Toyoda, Tetsuro and Wright, Derek W. and Daub, Carsten O. and Itoh, Masayoshi and Carninci, Piero and Hayashizaki, Yoshihide and Forrest, Alistair R. R. and Kawaji, Hideya},
abstractNote = {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/). In conclusion, 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.},
doi = {10.1186/s13059-014-0560-6},
journal = {GenomeBiology.com},
number = 1,
volume = 16,
place = {United States},
year = {Mon Jan 05 00:00:00 EST 2015},
month = {Mon Jan 05 00:00:00 EST 2015}
}
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https://doi.org/10.1186/s13059-014-0560-6
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    • Lorenzi, Lucía; Avila Cobos, Francisco; Decock, Anneleen
    • Genes, Chromosomes and Cancer, Vol. 58, Issue 4
    • DOI: 10.1002/gcc.22709

    Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain
    journal, January 2020

    Timing and localization of human dystrophin isoform expression provide insights into the cognitive phenotype of Duchenne muscular dystrophy
    journal, October 2017

    Repression of ferritin light chain translation by human eIF3
    journal, May 2019

    • Pulos-Holmes, Mia C.; Srole, Daniel N.; Lee, Amy S. Y.
    • eLife
    • DOI: 10.1101/316299

    Multiplexed dissection of a model human transcription factor binding site architecture
    posted_content, May 2019

    • Davis, Jessica E.; Insigne, Kimberly D.; Jones, Eric M.
    • BioRxiv
    • DOI: 10.1101/625434

    xCell: digitally portraying the tissue cellular heterogeneity landscape
    journal, November 2017

    CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness
    journal, June 2018

    The Stk35 locus contributes to normal gametogenesis and encodes a lncRNA responsive to oxidative stress
    journal, January 2018

    • Miyamoto, Yoichi; Whiley, Penny A. F.; Goh, Hoey Y.
    • Biology Open
    • DOI: 10.1242/bio.032631

    BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
    journal, January 2019

    The BioMart community portal: an innovative alternative to large, centralized data repositories.
    text, January 2015

    • Smedley, Damian; Haider, Syed; Durinck, Steffen
    • Apollo - University of Cambridge Repository
    • DOI: 10.17863/cam.57576

    Generation of Retinaldehyde for Retinoic Acid Biosynthesis
    journal, December 2019

    Virus-induced transposable element expression up-regulation in human and mouse host cells
    journal, January 2020

    • Macchietto, Marissa G.; Langlois, Ryan A.; Shen, Steven S.
    • Life Science Alliance, Vol. 3, Issue 2
    • DOI: 10.26508/lsa.201900536

    Unravelling the molecular basis for regulatory T-cell plasticity and loss of function in disease
    journal, January 2018

    • Sadlon, Timothy; Brown, Cheryl Y.; Bandara, Veronika
    • Clinical & Translational Immunology, Vol. 7, Issue 2
    • DOI: 10.1002/cti2.1011

    The adaptor protein ARA55 and the nuclear kinase HIPK1 assist c-Myb in recruiting p300 to chromatin
    journal, July 2017

    • Bengtsen, Mads; Sørensen, Linda; Aabel, Linn
    • Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1860, Issue 7
    • DOI: 10.1016/j.bbagrm.2017.05.001

    DNA methylation: an epigenetic mark of cellular memory
    journal, April 2017

    • Kim, Mirang; Costello, Joseph
    • Experimental & Molecular Medicine, Vol. 49, Issue 4
    • DOI: 10.1038/emm.2017.10

    IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients
    journal, April 2019

    NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network
    journal, April 2018

    CDK1 dependent phosphorylation of hTERT contributes to cancer progression
    journal, March 2020

    Familial Cancer Variant Prioritization Pipeline version 2 (FCVPPv2) applied to a papillary thyroid cancer family
    journal, August 2018

    • Kumar, Abhishek; Bandapalli, Obul Reddy; Paramasivam, Nagarajan
    • Scientific Reports, Vol. 8, Issue 1
    • DOI: 10.1038/s41598-018-29952-z

    Identification of chronological and photoageing-associated microRNAs in human skin
    journal, August 2018

    RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes
    journal, August 2017

    The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types
    journal, August 2017

    • Kawaji, Hideya; Kasukawa, Takeya; Forrest, Alistair
    • Scientific Data, Vol. 4, Issue 1
    • DOI: 10.1038/sdata.2017.113

    Correction: Corrigendum: Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos
    journal, September 2016

    • Madissoon, Elo; Jouhilahti, Eeva-Mari; Vesterlund, Liselotte
    • Scientific Reports, Vol. 6, Issue 1
    • DOI: 10.1038/srep32053

    Transcriptional control by enhancers and enhancer RNAs
    journal, October 2019

    Public data and open source tools for multi-assay genomic investigation of disease
    journal, October 2015

    • Kannan, Lavanya; Ramos, Marcel; Re, Angela
    • Briefings in Bioinformatics, Vol. 17, Issue 4
    • DOI: 10.1093/bib/bbv080

    An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays
    journal, September 2018

    • Mallik, Saurav; Odom, Gabriel J.; Gao, Zhen
    • Briefings in Bioinformatics, Vol. 20, Issue 6
    • DOI: 10.1093/bib/bby085

    FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki
    journal, January 2016

    On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase
    journal, January 2016

    RetrogeneDB–a database of plant and animal retrocopies
    journal, January 2017

    Assembly of a parts list of the human mitotic cell cycle machinery
    journal, November 2018

    • Giotti, Bruno; Chen, Sz-Hau; Barnett, Mark W.
    • Journal of Molecular Cell Biology, Vol. 11, Issue 8
    • DOI: 10.1093/jmcb/mjy063

    Ensembl 2016
    journal, December 2015

    • Yates, Andrew; Akanni, Wasiu; Amode, M. Ridwan
    • Nucleic Acids Research, Vol. 44, Issue D1
    • DOI: 10.1093/nar/gkv1157

    RNA damage in biological conflicts and the diversity of responding RNA repair systems
    journal, August 2016

    • Burroughs, A. Maxwell; Aravind, L.
    • Nucleic Acids Research, Vol. 44, Issue 18
    • DOI: 10.1093/nar/gkw722

    Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture
    journal, July 2017

    • Bouvy-Liivrand, Maria; Hernández de Sande, Ana; Pölönen, Petri
    • Nucleic Acids Research, Vol. 45, Issue 17
    • DOI: 10.1093/nar/gkx680

    MGA repository: a curated data resource for ChIP-seq and other genome annotated data
    journal, October 2017

    • Dréos, René; Ambrosini, Giovanna; Groux, Romain
    • Nucleic Acids Research, Vol. 46, Issue D1
    • DOI: 10.1093/nar/gkx995

    Update of the FANTOM web resource: expansion to provide additional transcriptome atlases
    journal, November 2018

    • Lizio, Marina; Abugessaisa, Imad; Noguchi, Shuhei
    • Nucleic Acids Research, Vol. 47, Issue D1
    • DOI: 10.1093/nar/gky1099

    Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing
    journal, October 2019

    • Bedi, Karan; Paulsen, Michelle T.; Wilson, Thomas E.
    • NAR Genomics and Bioinformatics, Vol. 2, Issue 1
    • DOI: 10.1093/nargab/lqz014

    PIVOT: Platform for Interactive Analysis and Visualization of Transcriptomics Data
    posted_content, July 2017

    • Zhu, Qin; Fisher, Stephen A.; Dueck, Hannah
    • BMC Bioinformatics
    • DOI: 10.1101/053348

    Deconvolution of Transcriptional Networks Identifies TCF4 as a Master Regulator in Schizophrenia
    preprint, June 2019

    • Torshizi, Abolfazl Doostparast; Armoskus, Chris; Zhang, Hanwen
    • DOI: 10.1101/133363

    Juxtacap Nucleotide Sequence Modulates eIF4E Binding and Translation
    posted_content, July 2017

    dyngen: a multi-modal simulator for spearheading new single-cell omics analyses
    journal, September 2020

    Cellular response to small molecules that selectively stall protein synthesis by the ribosome
    posted_content, November 2018

    • Liaud, Nadege; Horlbeck, Max A.; Gilbert, Luke A.
    • PLOS Genetics
    • DOI: 10.1101/461624

    Analysis of regulatory element evolution between human and mouse reveals a lack of cis-trans compensation
    preprint, November 2019

    • Mattioli, Kaia; Oliveros, Winona; Gerhardinger, Chiara
    • DOI: 10.1101/847491

    Pan‐cancer RNA‐seq data stratifies tumours by some hallmarks of cancer
    journal, January 2020

    • Frost, F. Graeme; Cherukuri, Praveen F.; Milanovich, Samuel
    • Journal of Cellular and Molecular Medicine, Vol. 24, Issue 1
    • DOI: 10.1111/jcmm.14746

    Type VII Collagen in the Human Accommodation System: Expression in Ciliary Body, Zonules, and Lens Capsule
    journal, February 2018

    • Wullink, Bart; Pas, Hendri H.; Van der Worp, Roelofje J.
    • Investigative Opthalmology & Visual Science, Vol. 59, Issue 2
    • DOI: 10.1167/iovs.17-23425

    DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism
    journal, December 2017

    Dichotomy in redundant enhancers points to presence of initiators of gene regulation
    journal, December 2018

    Application of hairless mouse strain to bioluminescence imaging of Arc expression in mouse brain
    journal, January 2017

    CpG promoter methylation of the ALKBH3 alkylation repair gene in breast cancer
    journal, July 2017

    • Stefansson, Olafur Andri; Hermanowicz, Stefan; van der Horst, Jasper
    • BMC Cancer, Vol. 17, Issue 1
    • DOI: 10.1186/s12885-017-3453-8

    Discovery of a novel long noncoding RNA overlapping the LCK gene that regulates prostate cancer cell growth
    journal, June 2019

    Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling
    journal, October 2016

    Patterns of ribosomal protein expression specify normal and malignant human cells
    journal, November 2016

    Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability
    journal, July 2017

    Systematic analysis of transcription start sites in avian development
    journal, September 2017

    metagene Profiles Analyses Reveal Regulatory Element’s Factor-Specific Recruitment Patterns
    journal, August 2016

    • Joly Beauparlant, Charles; Lamaze, Fabien C.; Deschênes, Astrid
    • PLOS Computational Biology, Vol. 12, Issue 8
    • DOI: 10.1371/journal.pcbi.1004751

    Discovery of gene regulatory elements through a new bioinformatics analysis of haploid genetic screens
    journal, January 2019

    RATA: A method for high-throughput identification of RNA bound transcription factors.
    journalarticle, January 2017

    • Schmidt, Karyn; Buquicchio, Frank; Carroll, Johanna S.
    • Journal of Biological Methods
    • DOI: 10.17863/cam.39227

    Generation of Retinaldehyde for Retinoic Acid Biosynthesis
    journal, December 2019

    Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences
    journal, March 2016

    • Moran, Sebastian; Arribas, Carles; Esteller, Manel
    • Epigenomics, Vol. 8, Issue 3
    • DOI: 10.2217/epi.15.114

    Virus-induced transposable element expression up-regulation in human and mouse host cells
    journal, January 2020

    • Macchietto, Marissa G.; Langlois, Ryan A.; Shen, Steven S.
    • Life Science Alliance, Vol. 3, Issue 2
    • DOI: 10.26508/lsa.201900536

    The relationships among bovine αS-casein phosphorylation isoforms suggest different phosphorylation pathways
    journal, October 2016

    • Fang, Z. H.; Visker, M. H. P. W.; Miranda, G.
    • Journal of Dairy Science, Vol. 99, Issue 10
    • DOI: 10.3168/jds.2016-11250

    Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line
    journal, November 2015

    HMGA2 Antisense Long Non-coding RNAs as New Players in the Regulation of HMGA2 Expression and Pancreatic Cancer Promotion
    journal, January 2020

    Shortage of Cellular ATP as a Cause of Diseases and Strategies to Enhance ATP
    journal, February 2019

    Epigenome Aberrations: Emerging Driving Factors of the Clear Cell Renal Cell Carcinoma
    journal, August 2017

    • Mehdi, Ali; Riazalhosseini, Yasser
    • International Journal of Molecular Sciences, Vol. 18, Issue 8
    • DOI: 10.3390/ijms18081774

    Long Non-Coding RNAs in Metabolic Organs and Energy Homeostasis
    journal, November 2017

    • Giroud, Maude; Scheideler, Marcel
    • International Journal of Molecular Sciences, Vol. 18, Issue 12
    • DOI: 10.3390/ijms18122578

    Computational analysis of brain transcriptome atlases
    text, January 2016

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