A promoter-level mammalian expression atlas

Forest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Baillie, J. Kenneth, De Hoon, Michael J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicholas, Jorgensen, 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, 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, Drablos, 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, Guh, 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 Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummer, 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, Takahash, Naoko, 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, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero and Hayashizaki, Yoshihide (2014) A promoter-level mammalian expression atlas. Nature, 507 7493: 462-470. doi:10.1038/nature13182

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Author Forest, Alistair R. R.
Kawaji, Hideya
Rehli, Michael
Baillie, J. Kenneth
De Hoon, Michael J. L.
Haberle, Vanja
Lassmann, Timo
Kulakovskiy, Ivan V.
Lizio, Marina
Itoh, Masayoshi
Andersson, Robin
Mungall, Christopher J.
Meehan, Terrence F.
Schmeier, Sebastian
Bertin, Nicholas
Jorgensen, 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
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
Drablos, 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
Guh, 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 Lima Morais, David A.
Morikawa, Hiromasa
Morimoto, Mitsuru
Moro, Kazuyo
Motakis, Efthymios
Motohashi, Hozumi
Mummer, 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
Takahash, Naoko
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, Vladimir B.
Taylor, Martin S.
Makeev, Vsevolod J.
Sandelin, Albin
Hume, David A.
Carninci, Piero
Hayashizaki, Yoshihide
Title A promoter-level mammalian expression atlas
Journal name Nature   Check publisher's open access policy
ISSN 0028-0836
1476-4687
Publication date 2014-01-01
Year available 2014
Sub-type Article (original research)
DOI 10.1038/nature13182
Open Access Status File (Author Post-print)
Volume 507
Issue 7493
Start page 462
End page 470
Total pages 9
Place of publication London, United Kingdom
Publisher Nature Publishing Group
Language eng
Subject 1000 General
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 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.
Keyword Multidisciplinary Sciences
Science & Technology - Other Topics
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

 
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