A promoter-level mammalian expression atlas
| Title: | A promoter-level mammalian expression atlas |
|---|---|
| Authors: | Forest, Alistair R R; Kawaji, Hideya; Rehli, Michael; Baillie, John Kenneth; De Hoon, Michiel Jl L; Haberle, Vanja; Lassmann, Timo; Kulakovskiy, Ivan V.; Lizio, Marina; Itoh, Masayoshi; Andersson, Robin; Iida, Kei; Ikawa, Tomokatsu; Jankovic, Boris R.; Jia, Hui; Joshi, Anagha Madhusudan; Jurman, Giuseppe; Kaczkowski, Bogumił; Kai, Chieko; Kaida, Kaoru; Kaiho, Ai; Mungall, Christopher J.; Kajiyama, Kazuhiro; Kanamori-Katayama, Mutsumi; Kasianov, Artem S.; Kasukawa, Takeya; Katayama, Shintaro; Kato, Sachi; Kawaguchi, Shuji; Kawamoto, Hiroshi; Kawamura, Yuki I.; Kawashima, Tsugumi; Meehan, Terrence F.; Kempfle, Judith S.; Kenna, Tony J.; Kere, Juha; Khachigian, Levon M.; Kitamura, Toshio; Klinken, Svend Peter; Knox, Alan; Kojima, Miki; Kojima, Soichi; Kondo, Naoto; Schmeier, Sebastian; Koseki, Haruhiko; Koyasu, Shigeo; Krampitz, Sarah; Kubosaki, Atsutaka; Kwon, Andrew T.; Laros, Jeroen F J; Lee, Weonju; Lennartsson, Andreas; Li, Kang; Lilje, Berit; Bertin, Nicolas; Lipovich, Leonard; MacKay-Sim, Alan; Manabe, Riichiroh; Mar, Jessica; Marchand, Benoit; Mathelier, Anthony; Mejhert, Niklas; Meynert, Alison M.; Mizuno, Yosuke; De Morais, David A Lima; Jørgensen, Mette Christine; Morikawa, Hiromasa; Morimoto, Mitsuru; Moro, Kazuyo; Motakis, Efthymios; Motohashi, Hozumi; Mummery, Christine L.; Murata, Mitsuyoshi; Nagao-Sato, Sayaka; Nakachi, Yutaka; Nakahara, Fumio; Dimont, Emmanuel; Nakamura, Toshiyuki; Nakamura, Yukio; Nakazato, Kenichi; Van Nimwegen, Erik; Ninomiya, Noriko; Nishiyori, Hiromi; Noma, Shohei; Nozaki, Tadasuke; Ogishima, Soichi; Ohkura, Naganari; Arner, Erik; Ohmiya, Hiroko; Ohno, Hiroshi; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Orlando, Valerio; Ovchinnikov, Dmitry A.; Pain, Arnab; Passier, Robert C J J; Patrikakis, Margaret; Schmidl, Christian; Persson, Helena A.; Piazza, Silvano; Prendergast, James G D; Rackham, Owen J L; Ramilowski, Jordan A.; Rashid, Mamoon; Ravasi, Timothy; Rizzu, Patrizia; Roncador, Marco; Roy, Sugata; Schaefer, Ulf; Rye, Morten Beck; Saijyo, Eri; Sajantila, Antti; Saka, Akiko; Sakaguchi, Shimon; Sakai, Mizuho; Sato, Hiroki; Satoh, Hironori; Savvi, Suzana; Saxena, Alka; Medvedeva, Yulia; Schneider, Claudio H.; Schultes, Erik A.; Schulze-Tanzil, Gundula G.; Schwegmann, Anita; Sengstag, Thierry; Sheng, Guojun; Shimoji, Hisashi; Shimoni, Yishai; Shin, Jay W.; Simon, Chris M.; Plessy, Charles; Sugiyama, Daisuke; Sugiyama, Takaaki; Suzuki, Masanori; Suzuki, Naoko; Swoboda, Rolf K.; 't Hoen, Peter Ac Chr; Tagami, Michihira; Tagami, Naokotakahashi; Takai, Jun; Tanaka, Hiroshi; Vitezic, Morana; Tatsukawa, Hideki; Tatum, Zuotian; Thompson, Mark; Toyoda, Hiroo; Toyoda, Tetsuro; Valen, Eivind; Van De Wetering, Marc L.; Van Den Berg, Linda M.; Verardo, Roberto; Vijayan, Dipti; Severin, Jessica M.; Vorontsov, Ilya E.; Wasserman, Wyeth W.; Watanabe, Shoko; Wells, Christine A.; Winteringham, Louise Natalie; Wolvetang, Ernst Jurgen; Wood, Emily J.; Yamaguchi, Yoko; Yamamoto, Masayuki; Yoneda, Misako; Semple, Colin Am M; Yonekura, Yohei; Yoshida, Shigehiro; Zabierowski, Susan E.; Zhang, Peter; Zhao, Xiaobei; Zucchelli, Silvia; Summers, Kim M.; Suzuki, Harukazu; Daub, Carsten Olivier; Kawai, Jun; Ishizu, Yuri; Heutink, Peter; Hide, Winston; Freeman, Tom C.; Lenhard, Boris; Bajic, Vladimir B.; Taylor, Martin S.; Makeev, Vsevolod J.; Sandelin, Albin; Hume, David A.; Carninci, Piero; Young, Robert S.; Hayashizaki, Yoshihide Yoshihide; Francescatto, Margherita; Alam, Intikhab; Albanese, Davide; Altschule, Gabriel M.; Arakawa, Takahiro; Archer, John A.C.; Arner, Peter; Babina, Magda; Rennie, Sarah; Balwierz, Piotr J.; Beckhouse, Anthony G.; Pradhan-Bhatt, Swati; Blake, Judith A.; Blumenthal, Antje; Bodega, Beatrice; Bonetti, Alessandro; Briggs, James A.; Brombacher, Frank; Burroughs, Alexander Maxwell; Califano, Andrea C.; Cannistraci, Carlo; Carbajo, Daniel; Chen, Yun; Chierici, Marco; Ciani, Yari; Clevers, Hans C.; Dalla, Emiliano; Davis, Carrie Anne; Detmar, Michael J.; Diehl, Alexander D.; Dohi, Taeko; Drabløs, Finn; Edge, Albert SB B; Edinger, Matthias G.; Ekwall, Karl; Endoh, Mitsuhiro; Enomoto, Hideki; Fagiolini, Michela; Fairbairn, Lynsey R.; Fang, Hai; Farach-Carson, Mary Cindy; Faulkner, Geoffrey J.; Favorov, Alexander V.; Fisher, Malcolm E.; Frith, Martin C.; Fujita, Rie; Fukuda, Shiro; Furlanello, Cesare; Furuno, Masaaki; Furusawa, Junichi; Geijtenbeek, Teunis Bh H; Gibson, Andrew P.; Gingeras, Thomas R.; Goldowitz, Dan; Gough, Julian; Guhl, Sven; Guler, Reto; Gustincich, Stefano; Ha, Thomas; Hamaguchi, Masahide; Hara, Mitsuko; Harbers, Matthias; Harshbarger, Jayson; Hasegawa, Akira; Hasegawa, Yuki; Hashimoto, Takehiro; Herlyn, Meenhard F.; Hitchens, Kelly J.; Sui, Shannan J Ho; Hofmann, Oliver M.; Hoof, Ilka; Hori, Fumi; Huminiecki, Łukasz B. |
| Contributors: | Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division; Environmental Science and Engineering Program; Applied Mathematics and Computational Science Program; Bioscience Program; Red Sea Research Center (RSRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Office of the VP; Research Applications; Research Computing; RIKEN, OSC, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan; RIKEN, CLST, DGT, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan; RIKEN, Prevent Med & Diag Innovat Program PMI, Wako, Saitama 3510198, Japan; Univ Hosp Regensburg, Dept Internal Med 3, D-93042 Regensburg, Germany; Regensburg Ctr Intervent Immunol RCI, D-93042 Regensburg, Germany; Univ Edinburgh, Roslin Inst, Edinburgh EH25 9RG, Midlothian, Scotland; Univ Edinburgh, Royal Dick Sch Vet Studies, Edinburgh EH25 9RG, Midlothian, Scotland; Univ Bergen, Dept Biol, NO-5006 Bergen, Norway; Univ London Imperial Coll Sci Technol & Med, Fac Med, Inst Clin Sci, MRC Clin Sci Ctr, London W12 0NN, England; Russian Acad Sci, VA Engelhardt Mol Biol Inst, Moscow 119991, Russia; Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia; Univ Copenhagen, Bioinformat Ctr, Dept Biol, DK-2200 Copenhagen, Denmark; Univ Copenhagen, BRIC, DK-2200 Copenhagen, Denmark; Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA; European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England; Massey Univ, North Shore Mail Ctr, Inst Nat & Math Sci, Auckland 0745, New Zealand; Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA; Karolinska Inst, Dept Cell & Mol Biol, SE-17177 Stockholm, Sweden; Univ Edinburgh, Western Gen Hosp, MRC Human Genet Unit, MRC IGMM, Edinburgh EH4 2XU, Midlothian, Scotland; Vrije Univ Amsterdam, Dept Clin Genet, Med Ctr Amsterdam, NL-1081 BT Amsterdam, Netherlands; Univ Porto, Grad Program Areas Basic & Appl Biol, Abel Salazar Biomed Sci Inst, P-4050313 Oporto, Portugal; Fdn Bruno Kessler, I-38123 Trento, Italy; Karolinska Inst, Dept Med, Karolinska Univ Hosp, SE-14186 Huddinge, Sweden; Univ Med Berlin, Dept Dermatol & Allergy, D-10117 Berlin, Germany; Univ Basel, Biozentrum, CH-4056 Basel, Switzerland; Univ Queensland, AIBN, St Lucia, Qld 4072, Australia; Univ Queensland, Australian Infect Dis Res Ctr AID, St Lucia, Qld 4072, Australia; Univ Delaware, Dept Biol Sci, Newark, DE 19713 USA; Jackson Lab, Bar Harbor, ME 04609 USA; Univ Queensland, Diamantina Inst, St Lucia, Qld 4072, Australia; IRCCS Fdn Santa Lucia, I-00143 Rome, Italy; Int Ctr Genet Engn & Biotechnol ICGEB Cape Town C, ZA-7925 Cape Town, South Africa; Univ Cape Town, Div Immunol, Inst Infect Dis & Mol Med IDM, ZA-7925 Cape Town, South Africa; Columbia Univ, Med Ctr, Dept Syst Biol, New York, NY 10032 USA; Columbia Univ, Med Ctr, Dept Biochem & Mol Biophys, New York, NY 10032 USA; Columbia Univ, Med Ctr, Dept Biomed Informat, New York, NY 10032 USA; Columbia Univ, Med Ctr, Herbert Irving Comprehens Canc Ctr, Inst Canc Genet, New York, NY 10032 USA; Albert Einstein Coll Med, Dept Syst & Computat Biol, Bronx, NY 10461 USA; LNCIB, I-34149 Trieste, Italy; Hubrecht Inst, NL-3584 CT Utrecht, Netherlands; Royal Netherlands Acad Arts & Sci, NL-1000 GC Amsterdam, Netherlands; Univ Med Ctr Utrecht, NL-3508 GA Utrecht, Netherlands; Cold Spring Harbor Lab, Cold Spring Harbor, NY 11797 USA; ETH, Inst Pharmaceut Sci, CH-8093 Zurich, Switzerland; SUNY Buffalo, Dept Neurol, Sch Med & Biomed Sci, New York State Ctr Excellence Bioinformat & Life, Buffalo, NY 14203 USA; Natl Ctr Global Hlth & Med, Res Ctr Hepatitis & Immunol Res Inst, Ichikawa, Chiba 2728516, Japan; Norwegian Univ Sci & Technol NTNU, Dept Canc Res & Mol Med, NO-7491 Trondheim, Norway; Harvard Univ, Sch Med, Massachusetts Eye & Ear Infirm, Dept Otol & Laryngol, Boston, MA 02114 USA; Karolinska Inst, Dept Biosci & Nutr, Ctr Biosci, SE-14183 Huddinge, Sweden; RIKEN, RCAI, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan; RIKEN, Ctr Integrat Med Sci, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan; RIKEN, CDB, Chuo Ku, Kobe, Hyogo 6500047, Japan; Harvard Univ, Sch Med, FM Kirby Neurobiol Ctr, Childrens Hosp Boston, Boston, MA 02115 USA; Univ Bristol, Dept Comp Sci, Bristol BS8 1UB, Avon, England; Rice Univ, Dept Biochem & Cell Biol, Houston, TX 77251 USA; Mater Med Res Inst, Cancer Biol Program, South Brisbane, Qld 4101, Australia; Johns Hopkins Univ, Sch Med, Dept Oncol, Div Oncol Biostat & Bioinformat, Baltimore, MD 21205 USA; State Res Inst Genet & Select Ind Microorganisms, Moscow 117545, Russia; Natl Inst Adv Ind Sci & Technol, Computat Biol Res Ctr, Koto Ku, Tokyo 1350064, Japan; Tohoku Univ, Dept Med Biochem, Grad Sch Med, Aoba Ku, Sendai, Miyagi 9808575, Japan; Keio Univ, Sch Med, Dept Microbiol & Immunol, Shinjuku Ku, Tokyo 1608582, Japan; Univ Amsterdam, Acad Med Ctr, NL-1105 AZ Amsterdam, Netherlands; Leiden Univ, Med Ctr, Dept Human Genet, NL-2333 ZC Leiden, Netherlands; Univ British Columbia, Dept Med Genet, Ctr Mol Med & Therapeut, Child & Family Res Inst, Vancouver, BC V5Z 4H4, Canada; SISSA, I-34136 Trieste, Italy; Osaka Univ, Immunol Frontier Res Ctr, Suita, Osaka 5650871, Japan; RIKEN, ASI, Wako, Saitama 3510198, Japan; Wistar Inst Anat & Biol, Melanoma Res Ctr, Philadelphia, PA 19104 USA; RIKEN, Bioinformat & Syst Engn Div BASE, Yokohama, Kanagawa 2300045, Japan; Wayne State Univ, Ctr Mol Med & Genet, Detroit, MI 48201 USA; Univ Tokyo, Lab Anim Res Ctr, Inst Med Sci, Minato Ku, Tokyo 1088639, Japan; Sci Life Lab, SE-17121 Solna, Sweden; Univ New S Wales, Ctr Vasc Res, Sydney, NSW 2052, Australia; Univ Tokyo, Div Cellular Therapy, Inst Med Sci, Tokyo 1088639, Japan; Univ Tokyo, Div Stem Cell Signaling, Inst Med Sci, Tokyo 1088639, Japan; Univ Western Australia, Harry Perkins Inst Med Res, QEII Med Ctr, Perth, WA 6009, Australia; Univ Western Australia, Med Res Ctr, QEII Med Ctr, Perth, WA 6009, Australia; Univ Nottingham, City Hosp, Nottingham NG5 1PB, England; Kyungpook Natl Univ, Sch Med, Dept Dermatol, Taegu 700721, South Korea; Griffith Univ, Natl Ctr Adult Stem Cell Res, Eskitis Inst Cell & Mol Therapies, Brisbane, Qld 4111, Australia; Saitama Med Univ, Div Funct Genom & Syst Med, Res Ctr Genom Med, Hidaka, Saitama 3501241, Japan; Univ Bristol, Fac Engn, Clifton BS81UB, England; Japanese Sci & Technol Agcy JST, PRESTO, Tokyo 1020076, Japan; Tohoku Univ, Ctr Radioisotope Sci, Grad Sch Med, Aoba Ku, Sendai, Miyagi 9808575, Japan; Leiden Univ, Med Ctr, NL-2300 RC Leiden, Netherlands; Saitama Med Univ, Div Translat Res, Res Ctr Genom Med, Hidaka, Saitama 3501241, Japan; RIKEN, BioResource Ctr BRC, Tsukuba, Ibaraki 3050074, Japan; Tokyo Univ Pharm & Life Sci, Dept Clin Mol Genet, Sch Pharm, Hachioji, Tokyo 1920392, Japan; Tokyo Med & Dent Univ, Dept Bioinformat, Med Res Inst, Bunkyo Ku, Tokyo 1138510, Japan; Ohu Univ, Dept Biochem, Sch Pharmaceut Sci, Koriyama, Fukushima 9638611, Japan |
| Publisher Information: | Springer Nature |
| Publication Year: | 2014 |
| Collection: | King Abdullah University of Science and Technology: KAUST Repository |
| Subject Terms: | Al |
| Description: | 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. ; 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. |
| Document Type: | article in journal/newspaper |
| File Description: | application/pdf |
| Language: | unknown |
| Relation: | (2014). A promoter-level mammalian expression atlas. Nature, 507(7493), 462–470. doi:10.1038/nature13182; Nature; http://hdl.handle.net/10754/565944 |
| DOI: | 10.1038/nature13182 |
| Availability: | http://hdl.handle.net/10754/565944; https://doi.org/10.1038/nature13182 |
| Accession Number: | edsbas.CCE742D |
| Database: | BASE |