Standard
A promoter-level mammalian expression atlas. / Forest, Alistair R.R.; Kawaji, Hideya; Rehli, Michael; Baillie, J. Kenneth; De Hoon, Michiel J.L.; Haberle, Vanja; Lassmann, Timo; Kulakovskiy, Ivan V.; Lizio, Marina; Itoh, Masayoshi; Andersson, Robin; Mungall, Christopher J.; Meehan, Terrence F.; Schmeier, Sebastian; Bertin, Nicolas; Jørgensen, Mette; Dimont, Emmanuel; Arner, Erik; Schmidl, Christian; Schaefer, Ulf; Medvedeva, Yulia A.; Plessy, Charles; Vitezic, Morana; Severin, Jessica; Semple, Colin A.; Ishizu, Yuri; Young, Robert S.; Francescatto, Margherita; Altschuler, Intikhab Alam; 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; Brombacher, Frank; Burroughs, A. Maxwell; Califano, Andrea; Cannistraci, Carlo V.; Carbajo, Daniel; Chen, Yun; Chierici, Marco; Ciani, Yari; Clevers, Hans C.; Dalla, Emiliano; Davis, Carrie A.; Detmar, Michael; Diehl, Alexander D.; Dohi, Taeko; Drabløs, Finn; Edge, Albert S B; Edinger, Matthias; Ekwall, Karl; Endoh, Mitsuhiro; Enomoto, Hideki; Fagiolini, Michela; Fairbairn, Lynsey; Fang, Hai; Farach-Carson, Mary C.; Faulkner, Geoffrey J.; Favorov, Alexander V.; Fisher, Malcolm E.; Frith, Martin C.; Fujita, Rie; Fukuda, Shiro; Furlanello, Cesare; Furuno, Masaaki; Furusawa, Jun Ichi; Geijtenbeek, Teunis B.; Gibson, Andrew P.; Gingeras, Thomas; Goldowitz, Daniel; Gough, Julian; Guhl, Sven; Guler, Reto; Gustincich, Stefano; Ha, Thomas J.; Hamaguchi, Masahide; Hara, Mitsuko; Harbers, Matthias; Harshbarger, Jayson; Hasegawa, Akira; Hasegawa, Yuki; Hashimoto, Takehiro; Herlyn, Meenhard; Hitchens, Kelly J.; Sui, Shannan J Ho; Hofmann, Oliver M.; Hoof, Ilka; Hori, Fumi; Huminiecki, Lukasz; Iida, Kei; Ikawa, Tomokatsu; Jankovic, Boris R.; Jia, Hui; Joshi, Anagha; Jurman, Giuseppe; Kaczkowski, Bogumil; Kai, Chieko; Kaida, Kaoru; Kaiho, Ai; Kajiyama, Kazuhiro; Kanamori-Katayama, Mutsumi; Kasianov, Artem S.; Kasukawa, Takeya; Katayama, Shintaro; Kato, Sachi; Kawaguchi, Shuji; Kawamoto, Hiroshi; Kawamura, Yuki I.; Kawashima, Tsugumi; Kempfle, Judith S.; Kenna, Tony J.; Kere, Juha; Khachigian, Levon M.; Kitamura, Toshio; Klinken, S. Peter; Knox, Alan J.; Kojima, Miki; Kojima, Soichi; Kondo, Naoto; Koseki, Haruhiko; Koyasu, Shigeo; Krampitz, Sarah; Kubosaki, Atsutaka; Kwon, Andrew T.; Laros, Jeroen F J; Lee, Weonju; Lennartsson, Andreas; Li, Kang; Lilje, Berit; Lipovich, Leonard; Mackay-sim, Alan; Manabe, Ri Ichiroh; Mar, Jessica C.; Marchand, Benoit; Mathelier, Anthony; Mejhert, Niklas; Meynert, Alison; Mizuno, Yosuke; De Morais, David A Lima; Morikawa, Hiromasa; Morimoto, Mitsuru; Moro, Kazuyo; Motakis, Efthymios; Motohashi, Hozumi; Mummery, Christine L.; Murata, Mitsuyoshi; Nagao-Sato, Sayaka; Nakachi, Yutaka; Nakahara, Fumio; Nakamura, Toshiyuki; Nakamura, Yukio; Nakazato, Kenichi; Van Nimwegen, Erik; Ninomiya, Noriko; Nishiyori, Hiromi; Noma, Shohei; Nozaki, Tadasuke; Ogishima, Soichi; Ohkura, Naganari; Ohmiya, Hiroko; Ohno, Hiroshi; Ohshima, Mitsuhiro; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Orlando, Valerio; Ovchinnikov, Dmitry A.; Pain, Arnab; Passier, Robert; Patrikakis, Margaret; Persson, Helena; Piazza, Silvano; Prendergast, James G D; Rackham, Owen J L; Ramilowski, Jordan A.; Rashid, Mamoon; Ravasi, Timothy; Rizzu, Patrizia; Roncador, Marco; Roy, Sugata; Rye, Morten B.; Saijyo, Eri; Sajantila, Antti; Saka, Akiko; Sakaguchi, Shimon; Sakai, Mizuho; Sato, Hiroki; Satoh, Hironori; Savvi, Suzana; Saxena, Alka; Schneider, Claudio; Schultes, Erik A.; Schulze-Tanzil, Gundula G.; Schwegmann, Anita; Sengstag, Thierry; Sheng, Guojun; Shimoji, Hisashi; Shimoni, Yishai; Shin, Jay W.; Simon, Christophe; Sugiyama, Daisuke; Sugiyama, Takaaki; Suzuki, Masanori; Suzuki, Naoko; Swoboda, Rolf K.; 'T Hoen, Peter A C; Tagami, Michihira; Tagami, Naoko Takahashi; Takai, Jun; Tanaka, Hiroshi; Tatsukawa, Hideki; Tatum, Zuotian; Thompson, Mark; Toyoda, Hiroo; Toyoda, Tetsuro; Valen, Eivind; Van De Wetering, Marc; Van Den Berg, Linda M.; Verardo, Roberto; Vijayan, Dipti; Vorontsov, Ilya E.; Wasserman, Wyeth W.; Watanabe, Shoko; Wells, Christine A.; Winteringham, Louise N.; Wolvetang, Ernst; Wood, Emily J.; Yamaguchi, Yoko; Yamamoto, Masayuki; Yoneda, Misako; Yonekura, Yohei; Yoshida, Shigehiro; Zabierowski, Susan E.; Zhang, Peter G.; Zhao, Xiaobei; Zucchelli, Silvia; Summers, Kim M.; Suzuki, Harukazu; Daub, Carsten O.; Kawai, Jun; Heutink, Peter; Hide, Winston; Freeman, Tom C.; Lenhard, Boris; Bajic, Lenhard Vladimir B; Taylor, Martin S.; Makeev, Vsevolod J.; Sandelin, Albin Gustav; Hume, David A.; Carninci, Piero; Hayashizaki, Yoshihide.
In:
Nature, Vol. 507, No. 7493, 2014, p. 462-470.
Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
Forest, ARR, Kawaji, H, Rehli, M, Baillie, JK, De Hoon, MJL, Haberle, V, Lassmann, T, Kulakovskiy, IV, Lizio, M, Itoh, M
, Andersson, R, Mungall, CJ, Meehan, TF, Schmeier, S, Bertin, N, Jørgensen, M, Dimont, E, Arner, E, Schmidl, C, Schaefer, U, Medvedeva, YA, Plessy, C, Vitezic, M, Severin, J, Semple, CA, Ishizu, Y, Young, RS, Francescatto, M, Altschuler, IA, Albanese, D, Altschule, GM, Arakawa, T, Archer, JAC, Arner, P, Babina, M, Rennie, S, Balwierz, PJ, Beckhouse, AG, Pradhan-Bhatt, S, Blake, JA, Blumenthal, A, Bodega, B, Bonetti, A, Briggs, J, Brombacher, F, Burroughs, AM, Califano, A, Cannistraci, CV, Carbajo, D, Chen, Y, Chierici, M, Ciani, Y, Clevers, HC, Dalla, E, Davis, CA, Detmar, M, Diehl, AD, Dohi, T, Drabløs, F, Edge, ASB, Edinger, M, Ekwall, K, Endoh, M, Enomoto, H, Fagiolini, M, Fairbairn, L, Fang, H, Farach-Carson, MC, Faulkner, GJ, Favorov, AV, Fisher, ME, Frith, MC, Fujita, R, Fukuda, S, Furlanello, C, Furuno, M, Furusawa, JI, Geijtenbeek, TB, Gibson, AP, Gingeras, T, Goldowitz, D, Gough, J, Guhl, S, Guler, R, Gustincich, S, Ha, TJ, Hamaguchi, M, Hara, M, Harbers, M, Harshbarger, J, Hasegawa, A, Hasegawa, Y, Hashimoto, T, Herlyn, M, Hitchens, KJ, Sui, SJH, Hofmann, OM, Hoof, I, Hori, F, Huminiecki, L, Iida, K, Ikawa, T, Jankovic, BR, Jia, H, Joshi, A, Jurman, G, Kaczkowski, B, Kai, C, Kaida, K, Kaiho, A, Kajiyama, K, Kanamori-Katayama, M, Kasianov, AS, Kasukawa, T, Katayama, S, Kato, S, Kawaguchi, S, Kawamoto, H, Kawamura, YI, Kawashima, T, Kempfle, JS, Kenna, TJ, Kere, J, Khachigian, LM, Kitamura, T, Klinken, SP, Knox, AJ, Kojima, M, Kojima, S, Kondo, N, Koseki, H, Koyasu, S, Krampitz, S, Kubosaki, A, Kwon, AT, Laros, JFJ, Lee, W, Lennartsson, A, Li, K, Lilje, B, Lipovich, L, Mackay-sim, A, Manabe, RI, Mar, JC, Marchand, B, Mathelier, A, Mejhert, N, Meynert, A, Mizuno, Y, De Morais, DAL, Morikawa, H, Morimoto, M, Moro, K, Motakis, E, Motohashi, H, Mummery, CL, Murata, M, Nagao-Sato, S, Nakachi, Y, Nakahara, F, Nakamura, T, Nakamura, Y, Nakazato, K, Van Nimwegen, E, Ninomiya, N, Nishiyori, H, Noma, S, Nozaki, T, Ogishima, S, Ohkura, N, Ohmiya, H, Ohno, H, Ohshima, M, Okada-Hatakeyama, M, Okazaki, Y, Orlando, V, Ovchinnikov, DA, Pain, A, Passier, R, Patrikakis, M, Persson, H, Piazza, S, Prendergast, JGD, Rackham, OJL, Ramilowski, JA, Rashid, M, Ravasi, T, Rizzu, P, Roncador, M, Roy, S, Rye, MB, Saijyo, E, Sajantila, A, Saka, A, Sakaguchi, S, Sakai, M, Sato, H, Satoh, H, Savvi, S, Saxena, A, Schneider, C, Schultes, EA, Schulze-Tanzil, GG, Schwegmann, A, Sengstag, T, Sheng, G, Shimoji, H, Shimoni, Y, Shin, JW, Simon, C, Sugiyama, D, Sugiyama, T, Suzuki, M, Suzuki, N, Swoboda, RK, 'T Hoen, PAC, Tagami, M, Tagami, NT, Takai, J, Tanaka, H, Tatsukawa, H, Tatum, Z, Thompson, M, Toyoda, H, Toyoda, T, Valen, E, Van De Wetering, M, Van Den Berg, LM, Verardo, R, Vijayan, D, Vorontsov, IE, Wasserman, WW, Watanabe, S, Wells, CA, Winteringham, LN, Wolvetang, E, Wood, EJ, Yamaguchi, Y, Yamamoto, M, Yoneda, M, Yonekura, Y, Yoshida, S, Zabierowski, SE, Zhang, PG, Zhao, X, Zucchelli, S, Summers, KM, Suzuki, H, Daub, CO, Kawai, J, Heutink, P, Hide, W, Freeman, TC, Lenhard, B, Bajic, LVB, Taylor, MS, Makeev, VJ
, Sandelin, AG, Hume, DA, Carninci, P & Hayashizaki, Y 2014, '
A promoter-level mammalian expression atlas',
Nature, vol. 507, no. 7493, pp. 462-470.
https://doi.org/10.1038/nature13182APA
Forest, A. R. R., Kawaji, H., Rehli, M., Baillie, J. K., De Hoon, M. J. L., Haberle, V., Lassmann, T., Kulakovskiy, I. V., Lizio, M., Itoh, M.
, Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jørgensen, M., Dimont, E., Arner, E., Schmidl, C., ... Hayashizaki, Y. (2014).
A promoter-level mammalian expression atlas.
Nature,
507(7493), 462-470.
https://doi.org/10.1038/nature13182Vancouver
Forest ARR, Kawaji H, Rehli M, Baillie JK, De Hoon MJL, Haberle V et al.
A promoter-level mammalian expression atlas.
Nature. 2014;507(7493):462-470.
https://doi.org/10.1038/nature13182Author
Forest, Alistair R.R. ; Kawaji, Hideya ; Rehli, Michael ; Baillie, J. Kenneth ; De Hoon, Michiel J.L. ; Haberle, Vanja ; Lassmann, Timo ; Kulakovskiy, Ivan V. ; Lizio, Marina ; Itoh, Masayoshi ; Andersson, Robin ; Mungall, Christopher J. ; Meehan, Terrence F. ; Schmeier, Sebastian ; Bertin, Nicolas ; Jørgensen, Mette ; Dimont, Emmanuel ; Arner, Erik ; Schmidl, Christian ; Schaefer, Ulf ; Medvedeva, Yulia A. ; Plessy, Charles ; Vitezic, Morana ; Severin, Jessica ; Semple, Colin A. ; Ishizu, Yuri ; Young, Robert S. ; Francescatto, Margherita ; Altschuler, Intikhab Alam ; 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 ; Brombacher, Frank ; Burroughs, A. Maxwell ; Califano, Andrea ; Cannistraci, Carlo V. ; Carbajo, Daniel ; Chen, Yun ; Chierici, Marco ; Ciani, Yari ; Clevers, Hans C. ; Dalla, Emiliano ; Davis, Carrie A. ; Detmar, Michael ; Diehl, Alexander D. ; Dohi, Taeko ; Drabløs, Finn ; Edge, Albert S B ; Edinger, Matthias ; Ekwall, Karl ; Endoh, Mitsuhiro ; Enomoto, Hideki ; Fagiolini, Michela ; Fairbairn, Lynsey ; Fang, Hai ; Farach-Carson, Mary C. ; Faulkner, Geoffrey J. ; Favorov, Alexander V. ; Fisher, Malcolm E. ; Frith, Martin C. ; Fujita, Rie ; Fukuda, Shiro ; Furlanello, Cesare ; Furuno, Masaaki ; Furusawa, Jun Ichi ; Geijtenbeek, Teunis B. ; Gibson, Andrew P. ; Gingeras, Thomas ; Goldowitz, Daniel ; Gough, Julian ; Guhl, Sven ; Guler, Reto ; Gustincich, Stefano ; Ha, Thomas J. ; Hamaguchi, Masahide ; Hara, Mitsuko ; Harbers, Matthias ; Harshbarger, Jayson ; Hasegawa, Akira ; Hasegawa, Yuki ; Hashimoto, Takehiro ; Herlyn, Meenhard ; Hitchens, Kelly J. ; Sui, Shannan J Ho ; Hofmann, Oliver M. ; Hoof, Ilka ; Hori, Fumi ; Huminiecki, Lukasz ; Iida, Kei ; Ikawa, Tomokatsu ; Jankovic, Boris R. ; Jia, Hui ; Joshi, Anagha ; Jurman, Giuseppe ; Kaczkowski, Bogumil ; Kai, Chieko ; Kaida, Kaoru ; Kaiho, Ai ; Kajiyama, Kazuhiro ; Kanamori-Katayama, Mutsumi ; Kasianov, Artem S. ; Kasukawa, Takeya ; Katayama, Shintaro ; Kato, Sachi ; Kawaguchi, Shuji ; Kawamoto, Hiroshi ; Kawamura, Yuki I. ; Kawashima, Tsugumi ; Kempfle, Judith S. ; Kenna, Tony J. ; Kere, Juha ; Khachigian, Levon M. ; Kitamura, Toshio ; Klinken, S. Peter ; Knox, Alan J. ; Kojima, Miki ; Kojima, Soichi ; Kondo, Naoto ; Koseki, Haruhiko ; Koyasu, Shigeo ; Krampitz, Sarah ; Kubosaki, Atsutaka ; Kwon, Andrew T. ; Laros, Jeroen F J ; Lee, Weonju ; Lennartsson, Andreas ; Li, Kang ; Lilje, Berit ; Lipovich, Leonard ; Mackay-sim, Alan ; Manabe, Ri Ichiroh ; Mar, Jessica C. ; Marchand, Benoit ; Mathelier, Anthony ; Mejhert, Niklas ; Meynert, Alison ; Mizuno, Yosuke ; De Morais, David A Lima ; Morikawa, Hiromasa ; Morimoto, Mitsuru ; Moro, Kazuyo ; Motakis, Efthymios ; Motohashi, Hozumi ; Mummery, Christine L. ; Murata, Mitsuyoshi ; Nagao-Sato, Sayaka ; Nakachi, Yutaka ; Nakahara, Fumio ; Nakamura, Toshiyuki ; Nakamura, Yukio ; Nakazato, Kenichi ; Van Nimwegen, Erik ; Ninomiya, Noriko ; Nishiyori, Hiromi ; Noma, Shohei ; Nozaki, Tadasuke ; Ogishima, Soichi ; Ohkura, Naganari ; Ohmiya, Hiroko ; Ohno, Hiroshi ; Ohshima, Mitsuhiro ; Okada-Hatakeyama, Mariko ; Okazaki, Yasushi ; Orlando, Valerio ; Ovchinnikov, Dmitry A. ; Pain, Arnab ; Passier, Robert ; Patrikakis, Margaret ; Persson, Helena ; Piazza, Silvano ; Prendergast, James G D ; Rackham, Owen J L ; Ramilowski, Jordan A. ; Rashid, Mamoon ; Ravasi, Timothy ; Rizzu, Patrizia ; Roncador, Marco ; Roy, Sugata ; Rye, Morten B. ; Saijyo, Eri ; Sajantila, Antti ; Saka, Akiko ; Sakaguchi, Shimon ; Sakai, Mizuho ; Sato, Hiroki ; Satoh, Hironori ; Savvi, Suzana ; Saxena, Alka ; Schneider, Claudio ; Schultes, Erik A. ; Schulze-Tanzil, Gundula G. ; Schwegmann, Anita ; Sengstag, Thierry ; Sheng, Guojun ; Shimoji, Hisashi ; Shimoni, Yishai ; Shin, Jay W. ; Simon, Christophe ; Sugiyama, Daisuke ; Sugiyama, Takaaki ; Suzuki, Masanori ; Suzuki, Naoko ; Swoboda, Rolf K. ; 'T Hoen, Peter A C ; Tagami, Michihira ; Tagami, Naoko Takahashi ; Takai, Jun ; Tanaka, Hiroshi ; Tatsukawa, Hideki ; Tatum, Zuotian ; Thompson, Mark ; Toyoda, Hiroo ; Toyoda, Tetsuro ; Valen, Eivind ; Van De Wetering, Marc ; Van Den Berg, Linda M. ; Verardo, Roberto ; Vijayan, Dipti ; Vorontsov, Ilya E. ; Wasserman, Wyeth W. ; Watanabe, Shoko ; Wells, Christine A. ; Winteringham, Louise N. ; Wolvetang, Ernst ; Wood, Emily J. ; Yamaguchi, Yoko ; Yamamoto, Masayuki ; Yoneda, Misako ; Yonekura, Yohei ; Yoshida, Shigehiro ; Zabierowski, Susan E. ; Zhang, Peter G. ; Zhao, Xiaobei ; Zucchelli, Silvia ; Summers, Kim M. ; Suzuki, Harukazu ; Daub, Carsten O. ; Kawai, Jun ; Heutink, Peter ; Hide, Winston ; Freeman, Tom C. ; Lenhard, Boris ; Bajic, Lenhard Vladimir B ; Taylor, Martin S. ; Makeev, Vsevolod J. ; Sandelin, Albin Gustav ; Hume, David A. ; Carninci, Piero ; Hayashizaki, Yoshihide. / A promoter-level mammalian expression atlas. In: Nature. 2014 ; Vol. 507, No. 7493. pp. 462-470.
Bibtex
@article{2c89639bb5874a318561c311c025ad12,
title = "A promoter-level mammalian expression atlas",
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 {\^a}{\~ } housekeeping{\^a} {\texttrademark}, 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.",
author = "Forest, {Alistair R.R.} and Hideya Kawaji and Michael Rehli and Baillie, {J. Kenneth} and {De Hoon}, {Michiel J.L.} and Vanja Haberle and Timo Lassmann and Kulakovskiy, {Ivan V.} and Marina Lizio and Masayoshi Itoh and Robin Andersson and Mungall, {Christopher J.} and Meehan, {Terrence F.} and Sebastian Schmeier and Nicolas Bertin and Mette J{\o}rgensen and Emmanuel Dimont and Erik Arner and Christian Schmidl and Ulf Schaefer and Medvedeva, {Yulia A.} and Charles Plessy and Morana Vitezic and Jessica Severin and Semple, {Colin A.} and Yuri Ishizu and Young, {Robert S.} and Margherita Francescatto and Altschuler, {Intikhab Alam} and Davide Albanese and Altschule, {Gabriel M.} and Takahiro Arakawa and Archer, {John A C} and Peter Arner and Magda Babina and Sarah Rennie and Balwierz, {Piotr J.} and Beckhouse, {Anthony G.} and Swati Pradhan-Bhatt and Blake, {Judith A.} and Antje Blumenthal and Beatrice Bodega and Alessandro Bonetti and James Briggs and Frank Brombacher and Burroughs, {A. Maxwell} and Andrea Califano and Cannistraci, {Carlo V.} and Daniel Carbajo and Yun Chen and Marco Chierici and Yari Ciani and Clevers, {Hans C.} and Emiliano Dalla and Davis, {Carrie A.} and Michael Detmar and Diehl, {Alexander D.} and Taeko Dohi and Finn Drabl{\o}s and Edge, {Albert S B} and Matthias Edinger and Karl Ekwall and Mitsuhiro Endoh and Hideki Enomoto and Michela Fagiolini and Lynsey Fairbairn and Hai Fang and Farach-Carson, {Mary C.} and Faulkner, {Geoffrey J.} and Favorov, {Alexander V.} and Fisher, {Malcolm E.} and Frith, {Martin C.} and Rie Fujita and Shiro Fukuda and Cesare Furlanello and Masaaki Furuno and Furusawa, {Jun Ichi} and Geijtenbeek, {Teunis B.} and Gibson, {Andrew P.} and Thomas Gingeras and Daniel Goldowitz and Julian Gough and Sven Guhl and Reto Guler and Stefano Gustincich and Ha, {Thomas J.} and Masahide Hamaguchi and Mitsuko Hara and Matthias Harbers and Jayson Harshbarger and Akira Hasegawa and Yuki Hasegawa and Takehiro Hashimoto and Meenhard Herlyn and Hitchens, {Kelly J.} and Sui, {Shannan J Ho} and Hofmann, {Oliver M.} and Ilka Hoof and Fumi Hori and Lukasz Huminiecki and Kei Iida and Tomokatsu Ikawa and Jankovic, {Boris R.} and Hui Jia and Anagha Joshi and Giuseppe Jurman and Bogumil Kaczkowski and Chieko Kai and Kaoru Kaida and Ai Kaiho and Kazuhiro Kajiyama and Mutsumi Kanamori-Katayama and Kasianov, {Artem S.} and Takeya Kasukawa and Shintaro Katayama and Sachi Kato and Shuji Kawaguchi and Hiroshi Kawamoto and Kawamura, {Yuki I.} and Tsugumi Kawashima and Kempfle, {Judith S.} and Kenna, {Tony J.} and Juha Kere and Khachigian, {Levon M.} and Toshio Kitamura and Klinken, {S. Peter} and Knox, {Alan J.} and Miki Kojima and Soichi Kojima and Naoto Kondo and Haruhiko Koseki and Shigeo Koyasu and Sarah Krampitz and Atsutaka Kubosaki and Kwon, {Andrew T.} and Laros, {Jeroen F J} and Weonju Lee and Andreas Lennartsson and Kang Li and Berit Lilje and Leonard Lipovich and Alan Mackay-sim and Manabe, {Ri Ichiroh} and Mar, {Jessica C.} and Benoit Marchand and Anthony Mathelier and Niklas Mejhert and Alison Meynert and Yosuke Mizuno and {De Morais}, {David A Lima} and Hiromasa Morikawa and Mitsuru Morimoto and Kazuyo Moro and Efthymios Motakis and Hozumi Motohashi and Mummery, {Christine L.} and Mitsuyoshi Murata and Sayaka Nagao-Sato and Yutaka Nakachi and Fumio Nakahara and Toshiyuki Nakamura and Yukio Nakamura and Kenichi Nakazato and {Van Nimwegen}, Erik and Noriko Ninomiya and Hiromi Nishiyori and Shohei Noma and Tadasuke Nozaki and Soichi Ogishima and Naganari Ohkura and Hiroko Ohmiya and Hiroshi Ohno and Mitsuhiro Ohshima and Mariko Okada-Hatakeyama and Yasushi Okazaki and Valerio Orlando and Ovchinnikov, {Dmitry A.} and Arnab Pain and Robert Passier and Margaret Patrikakis and Helena Persson and Silvano Piazza and Prendergast, {James G D} and Rackham, {Owen J L} and Ramilowski, {Jordan A.} and Mamoon Rashid and Timothy Ravasi and Patrizia Rizzu and Marco Roncador and Sugata Roy and Rye, {Morten B.} and Eri Saijyo and Antti Sajantila and Akiko Saka and Shimon Sakaguchi and Mizuho Sakai and Hiroki Sato and Hironori Satoh and Suzana Savvi and Alka Saxena and Claudio Schneider and Schultes, {Erik A.} and Schulze-Tanzil, {Gundula G.} and Anita Schwegmann and Thierry Sengstag and Guojun Sheng and Hisashi Shimoji and Yishai Shimoni and Shin, {Jay W.} and Christophe Simon and Daisuke Sugiyama and Takaaki Sugiyama and Masanori Suzuki and Naoko Suzuki and Swoboda, {Rolf K.} and {'T Hoen}, {Peter A C} and Michihira Tagami and Tagami, {Naoko Takahashi} and Jun Takai and Hiroshi Tanaka and Hideki Tatsukawa and Zuotian Tatum and Mark Thompson and Hiroo Toyoda and Tetsuro Toyoda and Eivind Valen and {Van De Wetering}, Marc and {Van Den Berg}, {Linda M.} and Roberto Verardo and Dipti Vijayan and Vorontsov, {Ilya E.} and Wasserman, {Wyeth W.} and Shoko Watanabe and Wells, {Christine A.} and Winteringham, {Louise N.} and Ernst Wolvetang and Wood, {Emily J.} and Yoko Yamaguchi and Masayuki Yamamoto and Misako Yoneda and Yohei Yonekura and Shigehiro Yoshida and Zabierowski, {Susan E.} and Zhang, {Peter G.} and Xiaobei Zhao and Silvia Zucchelli and Summers, {Kim M.} and Harukazu Suzuki and Daub, {Carsten O.} and Jun Kawai and Peter Heutink and Winston Hide and Freeman, {Tom C.} and Boris Lenhard and Bajic, {Lenhard Vladimir B} and Taylor, {Martin S.} and Makeev, {Vsevolod J.} and Sandelin, {Albin Gustav} and Hume, {David A.} and Piero Carninci and Yoshihide Hayashizaki",
year = "2014",
doi = "10.1038/nature13182",
language = "English",
volume = "507",
pages = "462--470",
journal = "Nature",
issn = "0028-0836",
publisher = "nature publishing group",
number = "7493",
}
RIS
TY - JOUR
T1 - A promoter-level mammalian expression atlas
AU - Forest, Alistair R.R.
AU - Kawaji, Hideya
AU - Rehli, Michael
AU - Baillie, J. Kenneth
AU - De Hoon, Michiel J.L.
AU - Haberle, Vanja
AU - Lassmann, Timo
AU - Kulakovskiy, Ivan V.
AU - Lizio, Marina
AU - Itoh, Masayoshi
AU - Andersson, Robin
AU - Mungall, Christopher J.
AU - Meehan, Terrence F.
AU - Schmeier, Sebastian
AU - Bertin, Nicolas
AU - Jørgensen, Mette
AU - Dimont, Emmanuel
AU - Arner, Erik
AU - Schmidl, Christian
AU - Schaefer, Ulf
AU - Medvedeva, Yulia A.
AU - Plessy, Charles
AU - Vitezic, Morana
AU - Severin, Jessica
AU - Semple, Colin A.
AU - Ishizu, Yuri
AU - Young, Robert S.
AU - Francescatto, Margherita
AU - Altschuler, Intikhab Alam
AU - Albanese, Davide
AU - Altschule, Gabriel M.
AU - Arakawa, Takahiro
AU - Archer, John A C
AU - Arner, Peter
AU - Babina, Magda
AU - Rennie, Sarah
AU - Balwierz, Piotr J.
AU - Beckhouse, Anthony G.
AU - Pradhan-Bhatt, Swati
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PY - 2014
Y1 - 2014
N2 - 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 â ̃ housekeepingâ ™, 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.
AB - 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 â ̃ housekeepingâ ™, 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.
U2 - 10.1038/nature13182
DO - 10.1038/nature13182
M3 - Journal article
C2 - 24670764
AN - SCOPUS:84897406127
VL - 507
SP - 462
EP - 470
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7493
ER -
