Gateways to the FANTOM5 promoter level mammalian expression atlas

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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/). 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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The online version of this article (doi:10.1186/s13059-014-0560-6) contains supplementary material, which is available to authorized users.

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Most cited references 35

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Gene Ontology: tool for the unification of biology

Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)

Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

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Genome-wide analysis of mammalian promoter architecture and evolution.

Piero Carninci, Albin Sandelin, Boris Lenhard … (2006)

Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.

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Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Y Takenaka, Rodrigo Nakamura, C Bult … (2002)

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

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Author and article information

Contributors

Marina Lizio: m.lizio@gsc.riken.jp

Jayson Harshbarger: jayson@gsc.riken.jp

Hisashi Shimoji: hisashi.shimoji@riken.jp

Jessica Severin: severin@gsc.riken.jp

Takeya Kasukawa: takeya.kasukawa@riken.jp

Serkan Sahin: serkan@gsc.riken.jp

Imad Abugessaisa: imad.abugessaisa@riken.jp

Shiro Fukuda: sfukuda@gsc.riken.jp

Fumi Hori: hori@gsc.riken.jp

Sachi Ishikawa-Kato: koishikawa@riken.jp

Christopher J Mungall: cjmungall@lbl.gov

Erik Arner: arner@gsc.riken.jp

J Kenneth Baillie: j.k.baillie@doctors.org.uk

Nicolas Bertin: nbertin@gsc.riken.jp

Hidemasa Bono: bono@dbcls.rois.ac.jp

Michiel de Hoon: mdehoon@gsc.riken.jp

Alexander D Diehl: addiehl@buffalo.edu

Emmanuel Dimont: edimont@mail.harvard.edu

Tom C Freeman: tfreeman@roslin.ed.ac.uk

Kaori Fujieda: kaorif@dbcls.rois.ac.jp

Winston Hide: whide@hsph.harvard.edu

Rajaram Kaliyaperumal: rr.kaliyaperumal@gmail.com

Toshiaki Katayama: ktym@dbcls.jp

Timo Lassmann: lassmann@gsc.riken.jp

Terrence F Meehan: tmeehan@ebi.ac.uk

Koro Nishikata: koro@base.riken.jp

Hiromasa Ono: hono@dbcls.rois.ac.jp

Michael Rehli: Michael.Rehli@klinik.uni-regensburg.de

Albin Sandelin: albin@binf.ku.dk

Erik A Schultes: schultes@hedgehogresearch.info

Peter AC ‘t Hoen: P.A.C._t_Hoen@lumc.nl

Zuotian Tatum: Z.Tatum@lumc.nl

Mark Thompson: mark9630@gmail.com

Tetsuro Toyoda: toyoda@base.riken.jp

Derek W Wright: Derek.Wright@roslin.ed.ac.uk

Carsten O Daub: daub@gsc.riken.jp

Masayoshi Itoh: maitoh@riken.jp

Piero Carninci: carninci@riken.jp

Yoshihide Hayashizaki: yosihide@gsc.riken.jp

Alistair RR Forrest: forrest@gsc.riken.jp

Hideya Kawaji: kawaji@gsc.riken.jp

Journal

Journal ID (nlm-ta): Genome Biol

Title: Genome Biology

Publisher: BioMed Central (London )

ISSN (Print): 1465-6906

ISSN (Electronic): 1465-6914

Publication date (Electronic): 5 January 2015

Publication date PMC-release: 5 January 2015

Publication date (Print): 2015

Volume: 16

Issue: 1

Electronic Location Identifier: 22

Affiliations

[ ]Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan

[ ]Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologie, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan

[ ]RIKEN Preventive Medicine and Diagnosis Innovation Program, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan

[ ]Preventive medicine and applied genomics unit, RIKEN Advanced Center for Computing and Communication, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan

[ ]Genomics Division, Lawrence Berkeley National Laboratory, 84R01, 1 Cyclotron Road, Berkeley, CA 94720 USA

[ ]Mouse Informatics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK

[ ]The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, EH25 9RG Scotland UK

[ ]Department of Human Genetics, BioSemantics Group, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA Netherlands

[ ]Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, Regensburg, D-93042 Germany

[ ]Database Center for Life Science, Research Organization of Information and Systems, 1111 Yata, Mishima, 411-8540 Japan

[ ]Department of Biology & Biotech Research and Innovation Centre, Section for Computational and RNA Biology, Copenhagen University, Ole Maaloes Vej 5, Copenhagen, N DK2200 Denmark

[ ]Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115 USA

[ ]Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, 701 Ellicott Street, Buffalo, NY 14203 USA

[ ]BioSemantics Group, Leiden Institute of Advanced Computer Science, Leiden University, 111 Snellius, Niels Bohrweg 1, Leiden, 2333 CA Netherlands

[ ]Database Center for Life Science, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0081 Japan

[ ]Integrated Database Unit, RIKEN Advanced Center for Computing and Communication, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan

[ ]Sheffield Institute for Translational Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield, S10 2HQ UK

[ ]Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008 Australia

[ ]Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599 Singapore

Article

Publisher ID: 560

DOI: 10.1186/s13059-014-0560-6

PMC ID: 4310165

PubMed ID: 25723102

SO-VID: a5340b16-138b-4868-b87e-11a630a69cd2

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 13 May 2014

Date accepted : 3 December 2014

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ScienceOpen disciplines: Genetics

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ScienceOpen disciplines: Genetics

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Gateways to the FANTOM5 promoter level mammalian expression atlas

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Abstract

Electronic supplementary material

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Nanopublications (single, attributable and machine-readable assertions in scientific literature)

Most cited references 35

Gene Ontology: tool for the unification of biology

Genome-wide analysis of mammalian promoter architecture and evolution.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Author and article information

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Cited by 377

Most referenced authors 3,552