The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line The FANTOM Consortium (Genome Network Project, Expression Cluster Workshop): Harukazu Suzuki* ,‡,≠,1 , Alistair R. R. Forrest* ,‡,≠,1,2 , Erik van Nimwegen* ,‡,≠,3 , Carsten O. Daub ‡,≠,1 , Piotr J. Balwierz ‡,3, Katharine M. Irvine ‡,≠,4,Timo Lassmann ‡,≠,1 , Timothy Ravasi ‡,≠,5, Yuki Hasegawa ‡,1 , Michiel J. L. de Hoon ‡,1 , Shintaro Katayama ‡,1 , Kate Schroder ‡,≠,4, Piero Carninci ‡,1 , Yasuhiro Tomaru ‡,1, Mutsumi Kanamori-Katayama ‡,1, Atsutaka Kubosaki ‡,1, Altuna Akalin 6, Yoshinari Ando 1, Erik Arner 1, Maki Asada 7, Hiroshi Asahara 7, Timothy Bailey 4, Vladimir B. Bajic ‡,8 , Denis Bauer 4, Anthony G. Beckhouse 2, Nicolas Bertin 1, Johan Björkegren 9, Frank Brombacher 10, Erika Bulger 1, Alistair M. Chalk 2, Joe Chiba 11, Nicole Cloonan 12 , Adam Dawe 8, Josee Dostie 13, Pär G. Engström 6, Magbubah Essack 8, Geoffrey J. Faulkner 12 , J Lynn Fink 14, David Fredman 6, Ko Fujimori 15 , Masaaki Furuno 1, Takashi Gojobori ‡,16 , Julian Gough 17 , Sean M. Grimmond ‡,12 , Mika Gustafsson 18, Megumi Hashimoto 7, Takehiro Hashimoto 1, Mariko Hatakeyama 19 , Susanne Heinzel 20, Winston Hide ‡,8,21 , Oliver Hofmann 8,21 , Michael Hörnquist 18, Lukasz Huminiecki 22 , Kazuho Ikeo 16 , Naoko Imamoto 23 , Satoshi Inoue 24 , Yusuke Inoue 25, Ryoko Ishihara 1, Takao Iwayanagi 26 , Anders Jacobsen 27 , Mandeep Kaur 8, Hideya Kawaji 1, Markus C. Kerr 14, Ryuichiro Kimura 11, Syuhei Kimura 28, Yasumasa Kimura 1, Hiroaki Kitano 29, Hisashi Koga 30 , Toshio Kojima 19 , Shinji Kondo 1, Takeshi Konno 16 , Anders Krogh 27 , Adele Kruger 8, Ajit Kumar 31 , Boris Lenhard ‡,6 , Andreas Lennartsson 1, Morten Lindow 27 , Marina Lizio 1, Cameron MacPherson 8, Norihiro Maeda 1, Christopher A. Maher 8, Monique Maqungo 8, Jessica Mar 32, Nicholas A. Matigian 2, Hideo Matsuda 33 , John S. Mattick 12 , Stuart Meier 8, Sei Miyamoto 16 , Etsuko Miyamoto-Sato 34 , Kazuhiko Nakabayashi 11, Yutaka Nakachi 35 , Mika Nakano 1, Sanne Nygaard 27 , Toshitsugu Okayama 16 , Yasushi Okazaki 35 , Haruka Okuda-Yabukami 1, Valerio Orlando 36 , Jun Otomo 37 , Mikhail Pachkov 3, Nikolai Petrovsky 20, Charles Plessy 1, John Quackenbush ‡,32 , Aleksandar Radovanovic 8, Michael Rehli 38, Rintaro Saito 39 , Albin Sandelin 27 , Sebastian Schmeier 8, Christian Schönbach 40 , Ariel S. Schwartz 5, Colin A. Semple 41 , Miho Sera 16 , Jessica Severin 1, Katsuhiko Shirahige 42, Cas Simons 12 , George St. Laurent 31 , Masanori Suzuki 1, Takahiro Suzuki 1, Matthew J. Sweet 43 , Ryan J. Taft 12 , Shizu Takeda 37 , Yoichi Takenaka 33 , Kai Tan 5, Martin S. Taylor 44, Rohan D. Teasdale 14, Jesper Tegnér ‡,9,45 , Sarah Teichmann 46 , Eivind Valen 27 , Claes Wahlestedt 47 , Kazunori Waki 1, Andrew Waterhouse 1, Christine A. Wells ‡,2 , Ole Winther 27 , Linda Wu 20 , Kazumi Yamaguchi 1, Hiroshi Yanagawa 34 , Jun Yasuda 1, Mihaela Zavolan 3, David A. Hume †,‡,≠,48 Riken Omics Science Center: Takahiro Arakawa 1, Shiro Fukuda 1, Kengo Imamura 1, Chikatoshi Kai 1, Ai Kaiho 1, Tsugumi Kawashima 1, Chika Kawazu 1, Yayoi Kitazume 1, Miki Kojima, 1 Hisashi Miura 1, Kayoko Murakami 1, Mitsuyoshi Murata 1, Noriko Ninomiya 1, Hiromi Nishiyori 1, Shohei Noma 1, Chihiro Ogawa 1, Takuma Sano 1, Christophe Simon 1, Michihira Tagami 1, Yukari Takahashi 1, Jun Kawai ‡,1 General Organizer: Yoshihide Hayashizaki †,‡,≠,1 *These authors contributed equally to this work. †To whom correspondence should be addressed. Email: [email protected] ‡These authors are core authors. ≠These authors are members of the FANTOM 4 headquarter. Affiliations: 1. RIKEN Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan. 2. The Eskitis Institute for Cell and Molecular Therapies, Griffith University, QLD 4111, Australia. 3. Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, CH-4056 Basel, 4056, Switzerland 4. Institute for Molecular Bioscience, The University of Queensland, Brisbane Qld, 4072, Australia - 2 - 5. Department of Bioengineering, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412 USA 6. Bergen Center for Computational Science, Høyteknologisenteret Thormøhlensgate 55, N-5008 Bergen, Norway 7. National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo 157-8535 8. South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17 , Bellville, 7535 South Africa 9. Computational Medicine Group, Atherosclerosis Research Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Solna SE- 171 76 Stockholm, Sweden 10. Institute of Infectious Disease and Molecular Medicine (IIDMM), Wolfson Pavilion Level 2, Faculty of Health Sciences, University of Cape Town, Observatory, 7925 11. Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510 Japan 12. Australian Research Council (ARC) Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia 13. Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6 Canada 14. Australian Research Council (ARC) Centre of Excellence in Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, 4072, Australia - 3 - 15. Laboratory of Biodefense and Regulation, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan 16. Research Organization of Information and Systems, Center for Information Biology and DNA Data Bank of Japan (DDBJ), National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan 17. Department of Computer Science, University of Bristol, Merchant Venturers Building, Woodland Road, Bristol, BS8 1UB, UK 18. Department of Science and Technology, Linköping University, SE-601 74 Norrköping, Sweden 19. Computational and Experimental Systems Biology Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho Tsurumi-ku Yokohama, Kanagawa, 230-0045 Japan 20. Department of Diabetes and Endcrinology, Flinders University and Medical Centre, Bedford Park, Adelaide, Australia 5042 21. Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, SPH2, 4th Floor, Boston, Massachusetts 02115, USA 22. Department of Cell and Molecular Biology (CMB) Karolinska Institutet P.O. Box 285 SE-171 77 Stockholm, Sweden 23. Cellular Dynamics Laboratory, Discovery and Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan 24. Graduate School of Medicine and Faculty of Medicine, the University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan - 4 - 25. Department of Biological and Chemical Engineering, Gunma University Faculty of Engineering, Tenjin-cho 1-5-1, Kiryu, Gunma 376-8515, Japan 26. R&D Solution Center, Research & Development Group, Hitachi, Ltd., 1-6-1, Marunouchi, Chiyodaku, Tokyo, 100-8220, Japan 27. The Bioinformatics Centre, Department of Biology and Biotech Research & Innovation Centre, University of Copenhagen, Ole Maloes Vej 5, DK-2200 Copenhagen N, Denmark 28. Department of Information and Knowledge Engineering, Faculty of Engineering , Tottori University, 4-101 Koyama-Minami, Tottori 680-8552 Japan 29. The Systems Biology Institute, 6-31-15 Jingumae M31 6A, Shibuya, Tokyo 150-0001 Japan 30. Department of Human Gene Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818 JAPAN 31. Department of Biochemistry and Molecular Biology, the George Washington University Medical Center, 2300 Eye St. N.W. Washington, D.C. 20037 U.S.A 32. Department of Biostatistics, Harvard School of Public Health, Dana-Farber Cancer Institute, Mayer 232, 44 Binney Street, Boston, MA 02115, USA 33. Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan 34. Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama 223-8522, Japan. - 5 - 35. Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical School, 1397-1 Yamane, Hidaka city, Saitama 350-1241, Japan 36. Dulbecco Telethon Institute, IRCCS Fondazione Santa Lucia at EBRI, Via del Fosso di Fiorano 64, 00143 Rome & IGB CNR, Via Pietro Castellino 111, 80131 Naples, Italy 37. Central Research Laboratory, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8601, Japan 38. Department of Hematology and Oncology, University of Regensburg, Hospital, 93042 Regensburg, Germany. 39. Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa 252-8520 Japan 40. School of Biological Science, Division of Genomics and Genetics, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 41. MRC Human Genetics Unit, Western, General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK 42. Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan 43. Institute for Molecular Bioscience, School of Molecular and Microbial Sciences, CRC for Chronic Inflammatory Diseases, The University of Queensland, St Lucia QLD 4072, AUSTRALIA