Article | Published:

A promoter-level mammalian expression atlas

Nature volume 507, pages 462470 (27 March 2014) | Download Citation

Abstract

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly ‘housekeeping’, whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

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Accessions

Primary accessions

DDBJ/GenBank/EMBL

Data deposits

All CAGE data has been deposited at DDBJ DRA under accession number DRA000991.

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Acknowledgements

FANTOM5 was made possible by a Research Grant for RIKEN Omics Science Center from MEXT to Y. Hayashizaki and a grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Y. Hayashizaki. It was also supported by Research Grants for RIKEN Preventive Medicine and Diagnosis Innovation Program (RIKEN PMI) to Y. Hayashizaki and RIKEN Centre for Life Science Technologies, Division of Genomic Technologies (RIKEN CLST (DGT)) from the MEXT, Japan. Extended acknowledgements are provided in the Supplementary Information.

Author information

Author notes

    • Christian Schmidl
    • , Yulia A. Medvedeva
    • , James Briggs
    • , Carlo V. Cannistraci
    • , Soichi Ogishima
    • , Hiroko Ohmiya
    •  & Alka Saxena

    Present addresses: Institute of Predictive and Personalized Medicine of Cancer, Ctra. de Can Roti, cami de les escoles, s/n, 08916 Badalona (Barcelona), Spain (Y.A.M.); Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Technische Universität Dresden, Dresden, Germany (C.V.C.); Genomics Core Facility, Biomedical Research Centre, Guy’s Hospital, London SE1 9RT, UK (A. Saxena); RIKEN Advanced Center for Computing and Communication (ACCC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan (H. Ohmiya); Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090 Vienna, Austria (C. Schmidl); Department of Biological and Biomedical Sciences, Harvard University, Cambridge, Massachusetts 02138, USA (J.B.); Department of Bioclinical Informatics,Tohoku Medical Megabank Organization,Tohoku University. Sendai 980-8573, Japan (S.O.).

    • Alistair R. R. Forrest
    • , Hideya Kawaji
    • , Michael Rehli
    •  & J. Kenneth Baillie

    These authors contributed equally to this work.

Affiliations

  1. RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

    • Alistair R. R. Forrest
    • , Hideya Kawaji
    • , Michiel J. L. de Hoon
    • , Timo Lassmann
    • , Marina Lizio
    • , Masayoshi Itoh
    • , Nicolas Bertin
    • , Erik Arner
    • , Charles Plessy
    • , Morana Vitezic
    • , Jessica Severin
    • , Yuri Ishizu
    • , Takahiro Arakawa
    • , Alessandro Bonetti
    • , A. Maxwell Burroughs
    • , Shiro Fukuda
    • , Masaaki Furuno
    • , Matthias Harbers
    • , Jayson Harshbarger
    • , Akira Hasegawa
    • , Yuki Hasegawa
    • , Takehiro Hashimoto
    • , Fumi Hori
    • , Bogumil Kaczkowski
    • , Kaoru Kaida
    • , Ai Kaiho
    • , Kazuhiro Kajiyama
    • , Mutsumi Kanamori-Katayama
    • , Shintaro Katayama
    • , Sachi Kato
    • , Tsugumi Kawashima
    • , Miki Kojima
    • , Naoto Kondo
    • , Atsutaka Kubosaki
    • , Andrew T. Kwon
    • , Ri-ichiroh Manabe
    • , Efthymios Motakis
    • , Mitsuyoshi Murata
    • , Sayaka Nagao-Sato
    • , Kenichi Nakazato
    • , Noriko Ninomiya
    • , Hiromi Nishiyori
    • , Shohei Noma
    • , Hiroko Ohmiya
    • , Jordan A. Ramilowski
    • , Sugata Roy
    • , Eri Saijyo
    • , Akiko Saka
    • , Mizuho Sakai
    • , Alka Saxena
    • , Thierry Sengstag
    • , Hisashi Shimoji
    • , Jay W. Shin
    • , Christophe Simon
    • , Masanori Suzuki
    • , Naoko Suzuki
    • , Michihira Tagami
    • , Naoko Takahashi
    • , Shoko Watanabe
    • , Shigehiro Yoshida
    • , Harukazu Suzuki
    • , Carsten O. Daub
    • , Jun Kawai
    • , Piero Carninci
    •  & Yoshihide Hayashizaki
  2. RIKEN Center for Life Science Technologies (Division of Genomic Technologies) (CLST (DGT)), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

    • Alistair R. R. Forrest
    • , Hideya Kawaji
    • , Michiel J. L. de Hoon
    • , Timo Lassmann
    • , Marina Lizio
    • , Masayoshi Itoh
    • , Nicolas Bertin
    • , Erik Arner
    • , Charles Plessy
    • , Jessica Severin
    • , Yuri Ishizu
    • , Takahiro Arakawa
    • , Alessandro Bonetti
    • , Masaaki Furuno
    • , Jayson Harshbarger
    • , Akira Hasegawa
    • , Yuki Hasegawa
    • , Fumi Hori
    • , Bogumil Kaczkowski
    • , Kaoru Kaida
    • , Kazuhiro Kajiyama
    • , Takeya Kasukawa
    • , Sachi Kato
    • , Tsugumi Kawashima
    • , Miki Kojima
    • , Naoto Kondo
    • , Andrew T. Kwon
    • , Ri-ichiroh Manabe
    • , Efthymios Motakis
    • , Mitsuyoshi Murata
    • , Hiromi Nishiyori
    • , Shohei Noma
    • , Hiroko Ohmiya
    • , Jordan A. Ramilowski
    • , Sugata Roy
    • , Mizuho Sakai
    • , Jay W. Shin
    • , Christophe Simon
    • , Naoko Suzuki
    • , Michihira Tagami
    • , Naoko Takahashi
    • , Shigehiro Yoshida
    • , Harukazu Suzuki
    •  & Piero Carninci
  3. RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.

    • Hideya Kawaji
    • , Masayoshi Itoh
    • , Jun Kawai
    •  & Yoshihide Hayashizaki
  4. Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany.

    • Michael Rehli
    • , Christian Schmidl
    •  & Matthias Edinger
  5. Regensburg Centre for Interventional Immunology (RCI), D-93042 Regensburg, Germany.

    • Michael Rehli
    •  & Matthias Edinger
  6. The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian EH25 9RG, UK.

    • J. Kenneth Baillie
    • , Lynsey Fairbairn
    • , Malcolm E. Fisher
    • , Anagha Joshi
    • , Kim M. Summers
    • , Tom C. Freeman
    •  & David A. Hume
  7. Department of Biology, University of Bergen, Thormøhlensgate 53, NO-5006 Bergen, Norway.

    • Vanja Haberle
  8. Faculty of Medicine, Institute of Clinical Sciences, MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK.

    • Vanja Haberle
    •  & Boris Lenhard
  9. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia.

    • Ivan V. Kulakovskiy
    •  & Vsevolod J. Makeev
  10. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin str. 3, Moscow 119991, Russia.

    • Ivan V. Kulakovskiy
    • , Yulia A. Medvedeva
    • , Alexander V. Favorov
    • , Artem S. Kasianov
    • , Ilya E. Vorontsov
    •  & Vsevolod J. Makeev
  11. The Bioinformatics Centre, Department of Biology and BRIC, University of Copenhagen, Ole Maaloes Vej 5, DK 2200 Copenhagen, Denmark.

    • Robin Andersson
    • , Mette Jørgensen
    • , Yun Chen
    • , Ilka Hoof
    • , Kang Li
    • , Berit Lilje
    • , Xiaobei Zhao
    •  & Albin Sandelin
  12. Genomics Division, Lawrence Berkeley National Laboratory, 84R01, 1 Cyclotron Road, Berkeley, California 94720, USA.

    • Christopher J. Mungall
  13. Mouse Informatics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

    • Terrence F. Meehan
  14. Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Ibn Al-Haytham Building -2, Thuwal 23955-6900, Kingdom of Saudi Arabia.

    • Sebastian Schmeier
    • , Ulf Schaefer
    • , Yulia A. Medvedeva
    • , Intikhab Alam
    • , John A. C. Archer
    • , Boris R. Jankovic
    • , Benoit Marchand
    • , Arnab Pain
    • , Mamoon Rashid
    •  & Vladimir B. Bajic
  15. Institute of Natural and Mathematical Sciences, Massey University, Private Bag 102-904, North Shore Mail Centre, 0745 Auckland, New Zealand.

    • Sebastian Schmeier
  16. Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, Massachusetts 02115, USA.

    • Emmanuel Dimont
    • , Gabriel M. Altschuler
    • , Shannan J. Ho Sui
    • , Oliver M. Hofmann
    •  & Winston Hide
  17. Department of Cell and Molecular Biology, Karolinska Institutet, P.O. Box 285, SE-171 77 Stockholm, Sweden.

    • Morana Vitezic
    •  & Lukasz Huminiecki
  18. MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine (MRC-IGMM), University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.

    • Colin A. Semple
    • , Robert S. Young
    • , Sarah Rennie
    • , Alison Meynert
    • , James G. D. Prendergast
    •  & Martin S. Taylor
  19. Department of Clinical Genetics, VU University Medical Center Amsterdam, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands.

    • Margherita Francescatto
    • , Patrizia Rizzu
    •  & Peter Heutink
  20. Graduate Program in Areas of Basic and Applied Biology, Abel Salazar Biomedical Sciences Institute, University of Porto, Rua de Jorge Viterbo Ferreira n. 228, 4050-313 Porto, Portugal.

    • Margherita Francescatto
  21. Predictive Models for Biomedicine and Environment, Fondazione Bruno Kessler, via Sommarive 18, 38123 Trento, Italy.

    • Davide Albanese
    • , Marco Chierici
    • , Cesare Furlanello
    • , Giuseppe Jurman
    •  & Marco Roncador
  22. Department of Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, SE-141 86 Huddinge, Sweden.

    • Peter Arner
    •  & Niklas Mejhert
  23. Department of Dermatology and Allergy, Charité Campus Mitte, Universitätsmedizin Berlin, Chariteplatz 1, 10117 Berlin, Germany.

    • Magda Babina
    •  & Sven Guhl
  24. Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.

    • Piotr J. Balwierz
    •  & Erik van Nimwegen
  25. Australian Institute for Bioengineering and Nanotechnology (AIBN), University of Queensland, Brisbane St Lucia, Queensland 4072, Australia.

    • Anthony G. Beckhouse
    • , James Briggs
    • , Kelly J. Hitchens
    • , Dmitry A. Ovchinnikov
    • , Dipti Vijayan
    • , Christine A. Wells
    •  & Ernst Wolvetang
  26. Australian Infectious Diseases Research Centre (AID), University of Queensland, Brisbane St Lucia, Queensland 4072, Australia.

    • Anthony G. Beckhouse
    • , Antje Blumenthal
    • , Kelly J. Hitchens
    • , Dipti Vijayan
    •  & Christine A. Wells
  27. Department of Biological Sciences, University of Delaware, Newark, Delaware 19713, USA.

    • Swati Pradhan-Bhatt
  28. Bioinformatics and Computational Biology, The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA.

    • Judith A. Blake
  29. Diamantina Institute, University of Queensland, Brisbane St Lucia, Queensland 4072, Australia.

    • Antje Blumenthal
    •  & Tony J. Kenna
  30. IRCCS Fondazione Santa Lucia, via del Fosso di Fiorano 64, 00143 Rome, Italy.

    • Beatrice Bodega
    •  & Valerio Orlando
  31. Immunology and Infectious Disease, International Centre for Genetic Engineering & Biotechnology (ICGEB) Cape Town component, Anzio Road, Observatory 7925, Cape Town, South Africa.

    • Frank Brombacher
    • , Reto Guler
    • , Suzana Savvi
    •  & Anita Schwegmann
  32. Division of Immunology, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Anzio Road, Observatory 7925, Cape Town, South Africa.

    • Frank Brombacher
    • , Reto Guler
    • , Suzana Savvi
    •  & Anita Schwegmann
  33. Department of Systems Biology, Columbia University Medical Center, 1130 St. Nicholas Avenue, New York, New York 10032, USA.

    • Andrea Califano
  34. Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, 701 West 168th Street, New York, New York 10032, USA.

    • Andrea Califano
  35. Department of Biomedical Informatics, Columbia University Medical Center, 622 West 168th Street, VC5, New York, New York 10032, USA.

    • Andrea Califano
  36. Institute of Cancer Genetics, Columbia University Medical Center, Herbert Irving Comprehensive Cancer Center, 1130 St. Nicholas Avenue, New York, New York 10032, USA.

    • Andrea Califano
    •  & Yishai Shimoni
  37. Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Ibn Al-Haytham Building -2, Thuwal 23955-6900, Kingdom of Saudi Arabia.

    • Carlo V. Cannistraci
    • , Valerio Orlando
    • , Arnab Pain
    • , Mamoon Rashid
    •  & Timothy Ravasi
  38. Applied Mathematics and Computational Science Program, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.

    • Carlo V. Cannistraci
    •  & Timothy Ravasi
  39. Department of Systems and Computational Biology, Albert Einstein College of Medicine, The Bronx, New York, New York 10461, USA.

    • Daniel Carbajo
    •  & Jessica C. Mar
  40. Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie (LNCIB), Padriciano 99, 34149 Trieste, Italy.

    • Yari Ciani
    • , Emiliano Dalla
    • , Silvano Piazza
    • , Claudio Schneider
    •  & Roberto Verardo
  41. Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.

    • Hans C. Clevers
    •  & Marc van de Wetering
  42. The Royal Netherlands Academy of Arts and Sciences, P.O. Box 19121, NL-1000 GC Amsterdam, The Netherlands.

    • Hans C. Clevers
  43. University Medical Centre Utrecht, Postbus 85500, 3508 GA Utrecht, The Netherlands.

    • Hans C. Clevers
  44. Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11797, USA.

    • Carrie A. Davis
    •  & Thomas Gingeras
  45. Institute of Pharmaceutical Sciences, ETH Zurich, Vladimir-Prelog-Weg 3, HCI H 303, 8093 Zurich, Switzerland.

    • Michael Detmar
    •  & Sarah Krampitz
  46. Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, USA.

    • Alexander D. Diehl
  47. Gastroenterology, Research Center for Hepatitis and Immunology Research Institute, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan.

    • Taeko Dohi
    •  & Yuki I. Kawamura
  48. Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), P.O. Box 8905, NO-7491 Trondheim, Norway.

    • Finn Drabløs
    •  & Morten B. Rye
  49. Department of Otology and Laryngology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Eaton-Peabody Lab, 243 Charles Street, Boston, Massachusetts 02114, USA.

    • Albert S. B. Edge
    •  & Judith S. Kempfle
  50. Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet, Hälsovägen 7-9, SE-141 83 Huddinge, Sweden.

    • Karl Ekwall
    • , Juha Kere
    • , Andreas Lennartsson
    •  & Helena Persson
  51. RIKEN Research Center for Allergy and Immunology (RCAI), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

    • Mitsuhiro Endoh
    • , Jun-ichi Furusawa
    • , Tomokatsu Ikawa
    • , Hiroshi Kawamoto
    • , Haruhiko Koseki
    • , Shigeo Koyasu
    • , Kazuyo Moro
    • , Hiroshi Ohno
    •  & Mariko Okada-Hatakeyama
  52. RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

    • Mitsuhiro Endoh
    • , Jun-ichi Furusawa
    • , Tomokatsu Ikawa
    • , Haruhiko Koseki
    • , Shigeo Koyasu
    • , Kazuyo Moro
    • , Hiroshi Ohno
    •  & Mariko Okada-Hatakeyama
  53. RIKEN Center for Developmental Biology (CDB), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.

    • Hideki Enomoto
    • , Mitsuru Morimoto
    • , Guojun Sheng
    •  & Yohei Yonekura
  54. FM Kirby Neurobiology Center, Children’s Hospital Boston, Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA.

    • Michela Fagiolini
  55. Department of Computer Science, University of Bristol, Merchant Venturers Building, Woodland Road, Bristol BS8 1UB, UK.

    • Hai Fang
    • , Julian Gough
    •  & Owen J. L. Rackham
  56. Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251-1892, USA.

    • Mary C. Farach-Carson
  57. Cancer Biology Program, Mater Medical Research Institute, Raymond Terrace, South Brisbane, Queensland 4101, Australia.

    • Geoffrey J. Faulkner
  58. Department of Oncology, Division of Oncology, Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, 550 North Broadway, Baltimore, Maryland 21205, USA.

    • Alexander V. Favorov
  59. State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika, 1-st Dorozhniy pr., 1, 117545 Moscow, Russia.

    • Alexander V. Favorov
  60. Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.

    • Martin C. Frith
  61. Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.

    • Rie Fujita
    • , Hironori Satoh
    • , Jun Takai
    •  & Masayuki Yamamoto
  62. Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo 160-8582, Japan.

    • Jun-ichi Furusawa
    • , Shigeo Koyasu
    •  & Kazuyo Moro
  63. Experimental Immunology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.

    • Teunis B. Geijtenbeek
    •  & Linda M. van den Berg
  64. Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands.

    • Andrew P. Gibson
    • , Jeroen F. J. Laros
    • , Erik A. Schultes
    • , Peter A. C. ’t Hoen
    • , Zuotian Tatum
    •  & Mark Thompson
  65. Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, British Columbia V5Z 4H4, Canada.

    • Daniel Goldowitz
    • , Thomas J. Ha
    • , Anthony Mathelier
    • , Wyeth W. Wasserman
    •  & Peter G. Zhang
  66. Neuroscience, SISSA, via Bonomea 265, 34136 Trieste, Italy.

    • Stefano Gustincich
    •  & Silvia Zucchelli
  67. Experimental Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan.

    • Masahide Hamaguchi
    • , Hiromasa Morikawa
    • , Naganari Ohkura
    •  & Shimon Sakaguchi
  68. RIKEN Advanced Science Institute (ASI), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.

    • Mitsuko Hara
    •  & Soichi Kojima
  69. Melanoma Research Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA.

    • Meenhard Herlyn
    • , Rolf K. Swoboda
    •  & Susan E. Zabierowski
  70. RIKEN Bioinformatics And Systems Engineering Division (BASE), 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.

    • Kei Iida
    • , Shuji Kawaguchi
    •  & Tetsuro Toyoda
  71. Center for Molecular Medicine and Genetics, Wayne State University, 3228 Scott Hall, 540 East Canfield Street, Detroit, Michigan 48201-1928, USA.

    • Hui Jia
    • , Leonard Lipovich
    •  & Emily J. Wood
  72. Laboratory Animal Research Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

    • Chieko Kai
    • , Toshiyuki Nakamura
    • , Hiroki Sato
    • , Takaaki Sugiyama
    •  & Misako Yoneda
  73. Science for Life Laboratory, Box 1031, SE-171 21 Solna, Sweden.

    • Juha Kere
  74. Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia.

    • Levon M. Khachigian
    •  & Margaret Patrikakis
  75. Division of Cellular Therapy and Division of Stem Cell Signaling, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan.

    • Toshio Kitamura
    •  & Fumio Nakahara
  76. Harry Perkins Institute of Medical Research, and the Centre for Medical Research, University of Western Australia, QQ Block, QEII Medical Centre, Nedlands, Perth, Western Australia 6009, Australia.

    • S. Peter Klinken
    •  & Louise N. Winteringham
  77. Respiratory Medicine, University of Nottingham, Clinical Sciences Building, City Hospital, Hucknall Road, Nottingham NG5 1PB, UK.

    • Alan J. Knox
  78. Department of Dermatology, Kyungpook National University School of Medicine, 130 Dongdeok-ro Jung-gu, Daegu 700-721, South Korea.

    • Weonju Lee
  79. National Centre for Adult Stem Cell Research, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Queensland 4111, Australia.

    • Alan Mackay-sim
  80. Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama 350-1241, Japan.

    • Yosuke Mizuno
    • , Yutaka Nakachi
    •  & Yasushi Okazaki
  81. Faculty of Engineering, University of Bristol, Merchant Venturers Building, Woodland Road, Clifton BS8 1UB, UK.

    • David A. de Lima Morais
  82. PRESTO, Japanese Science and Technology Agency (JST), 7 Gobancho, Chiyodaku, Tokyo 102-0076, Japan.

    • Kazuyo Moro
  83. Center for Radioisotope Sciences, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.

    • Hozumi Motohashi
  84. Anatomy and Embryology, Leiden University Medical Center, Einthovenweg 20, P.O. Box 9600, 2300 RC Leiden, The Netherlands.

    • Christine L. Mummery
    •  & Robert Passier
  85. Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama 350-1241, Japan.

    • Yutaka Nakachi
    •  & Yasushi Okazaki
  86. RIKEN BioResource Center (BRC), Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan.

    • Yukio Nakamura
  87. Department of Clinical Molecular Genetics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.

    • Tadasuke Nozaki
    •  & Hiroo Toyoda
  88. Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.

    • Soichi Ogishima
    •  & Hiroshi Tanaka
  89. Department of Biochemistry, Ohu University School of Pharmaceutical Sciences, Misumido 31-1, Tomitamachi, Koriyama, Fukushima 963-8611, Japan.

    • Mitsuhiro Ohshima
  90. Hjelt Institute, Department of Forensic Medicine, University of Helsinki, Kytosuontie 11, 003000 Helsinki, Finland.

    • Antti Sajantila
  91. DSMB Dipartimento Scienze Mediche e Biologiche University of Udine, P.le Kolbe 3, 33100 Udine, Italy.

    • Claudio Schneider
  92. Department of Orthopedic, Trauma and Reconstructive Surgery, Charité Universitätsmedizin Berlin, Garystrasse 5, 14195 Berlin, Germany.

    • Gundula G. Schulze-Tanzil
  93. Center for Clinical and Translational Reseach, Kyushu University Hospital, Station for Collaborative Research1 4F, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan.

    • Daisuke Sugiyama
  94. Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan.

    • Hideki Tatsukawa
  95. Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA.

    • Eivind Valen
  96. Department of Biochemistry, Nihon University School of Dentistry, 1-8-13, Kanda-Surugadai, Chiyoda-ku, Tokyo 101-8310, Japan.

    • Yoko Yamaguchi
  97. Department of Informatics, University of Bergen, Høgteknologisenteret, Thormøhlensgate 53, NO-5008 Bergen, Norway.

    • Boris Lenhard
  98. Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (MIPT) 9, Institutsky Per., Dolgoprudny, Moscow Region 141700, Russia.

    • Vsevolod J. Makeev

Consortia

  1. The FANTOM Consortium and the RIKEN PMI and CLST (DGT)

Authors

    Contributions

    The core members of FANTOM5 phase 1 were Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Timo Lassmann, Masayoshi Itoh, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci and Yoshihide Hayashizaki. Samples were provided by: A. Blumenthal, A. Bonetti, A. Mackay-sim, A. Sajantila, A. Saxena, A. Schwegmann, A.G.B., A.J.K., A.L., A.R.R.F., A.S.B.E., B.B., C. Schmidl, C. Schneider, C.A.D., C.A.W., C.K., C.L.M., D.A.H., D.A.O., D.G., D.S., D.V., E.W., F.B., F.N., G.G.S., G.J.F., G.S., H. Kawamoto, H. Koseki, H. Morikawa, H. Motohashi, H. Ohno, H. Sato, H. Satoh, H. Tanaka, H. Tatsukawa, H. Toyoda, H.C.C., H.E., J. Kere, J.B., J.F., J.K.B., J.S.K., J.T., J.W.S., K.E., K.J.H., K.M., K.M.S., L.F., L.M.K., L.M.vdB., L.N.W., M. Edinger, M. Endoh, M. Fagiolini, M. Hamaguchi, M. Hara, M. Herlyn, M. Morimoto, M. Rehli, M. Yamamoto, M. Yoneda, M.B., M.C.F.C., M.D., M.E.F., M.O., M.O.H., M.P., M.vdW., N.M., N.O., N.T., P.A., P.G.Z., P.H., P.R., R.F., R.G., R.K.S., R.P., R.V., S. Guhl, S. Gustincich, S. Kojima, S. Koyasu, S. Krampitz, S. Sakaguchi, S. Savvi, S.E.Z., S.O., S.P.B., S.P.K., S. Roy., S.Z., T. Kitamura, T. Nakamura, T. Nozaki, T. Sugiyama, T.B.G., T.D., T.G., T.I., T.J.H., T.J.K., V.O., W.L., Y. Hasegawa, Y. Nakachi, Y. Nakamura, Y. Yamaguchi, Y. Yonekura, Y.I., Y.I.K., Y.M. and Y.O. Analyses were carried out by: A. Mathelier, A. Meynert, A. Sandelin, A.C., A.D.D., A.P.G., A.H., A.J., A.M.B., A.P., A.R.R.F., A.S.K., A.T.K., A.V.F., B. Lenhard, B. Lilje, B.D., B.K., B.M., B.R.J., C. Schmidl, C. Schneider, C.A.S., C.F., C.J.M., C.O.D., C.P., C.V.C., D.A., D.A.M., D.C., E. Dalla, E. Dimont, E.A., E.A.S., E.J.W., E.M., E.V., Ev.N., F.D., G.J., G.J.F., G.M.A., H. Kawaji, H. Ohmiya, H. Shimoji, H.F., H.J., H.P., I.A., I.E.V., I.H., I.V.K., J.A.B., J.A.C.A., J.A.R., J.C.M., J.F.J.L., J.G., J.G.D.P., J.H., J.K.B., J.S., K. Kajiyama, K.I., K.L., L.H., L.L., M. Francescatto, M. Rashid, M. Rehli, M. Roncador, M. Thompson, M.B.R., M.C., M.C.F., M.J., M.J.L.dH., M.L., M.S.T., M.V., N.B., O.J.L.R., O.M.H., P.A.C.tH., P.J.B, R.A., R.S.Y., S. Katayama, S. Kawaguchi, S. Schmeier, S. Rennie, S.F., S.J.H.S., S.P., T. Sengstag, T.C.F., T.F.M., T.H., T.K., T.L., T.R., T.T., U.S., V.B.B., V.H., V.J.M., W.H., W.W.W., X.Z., Y. Chen, Y. Ciani, Y.A.M., Y.S., Z.T. Libraries were generated by: A. Kaiho, A. Kubosaki, A. Saka, C. Simon, E.S., F.H., H.N., J. Kawai, K. Kaida, K.N., M. Furuno, M. Murata, M. Sakai, M. Tagami, M.I., M.K., M.K.K., N.K., N.N., N.S., P.C., R.M., S. Kato, S.N., S.N.-S., S.W., S.Y., T.A., T. Kawashima. The manuscript was written by A.R.R.F. and D.A.H. with help from A. Sandelin, J.K.B., M. Rehli, H.K., M.J.L.dH., V.H., I.V.K., M.T. and K.M.S. with contributions, edits and comments from all authors. The project was managed by Y. Hayashizaki, A.R.R.F., P.C., M.I., M.S., J. Kawai, C.O.D., H. Suzuki, T.L. and N.K. The scientific coordinator was A.R.R.F and the general organizer was Y. Hayashizaki.

    Competing interests

    The author declare no competing financial interests.

    Corresponding authors

    Correspondence to Alistair R. R. Forrest or Piero Carninci or Yoshihide Hayashizaki.

    Extended data

    Supplementary information

    PDF files

    1. 1.

      Supplementary Information

      This file contains Acknowledgements, Supplementary Methods, Supplementary Notes 1-7, Supplementary Figures 1-24, and additional references (see page 1 for more details). Supplementary Tables 1-16 are in a separate excel fie.

    Excel files

    1. 1.

      Supplementary Tables

      This file contains Supplementary Tables 1-16.Supplementary Table 2 in the original file was truncated and was replace online on 19 October 2015.

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    DOI

    https://doi.org/10.1038/nature13182

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