FANTOM5 Papers

  • A promoter level mammalian expression atlas.

    Cap Analysis of Gene Expression (CAGE) across a large collection of primary cell types has revealed many mammalian promoters are composite entities composed of multiple closely-separated TSS, with independent cell-type-specific expression profiles. The FANTOM5 promoter centric expression atlas provides expression profiles for the majority of coding and non-coding transcripts in the human and mouse genomes.

    Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. Semple, Yuri Ishizu, Robert S. Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, Takahiro Arakawa, John A. C. Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J. Balwierz, Anthony G. Beckhouse, Swati Pradhan-Bhatt, Judith A. Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans C. Clevers, Emiliano Dalla, Carrie A. Davis, Michael Detmar, Alexander D. Diehl, Taeko Dohi, Finn Drabløs, Albert S. B. Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C. Farach-Carson, Geoffrey J. Faulkner, Alexander V. Favorov, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J. Hitchens, Shannan J. Ho Sui, Oliver M. Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R. Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S. Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I. Kawamura, Tsugumi Kawashima, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, S. Peter Klinken, Alan J. Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T. Kwon, Jeroen F. J. Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-sim, Ri-ichiroh Manabe, Jessica C. Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison Meynert, Yosuke Mizuno, David A. de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine L.Mummery, Mitsuyoshi Murata, Sayaka Nagao-Sato, Yutaka Nakachi, FumioNakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik vanNimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, TadasukeNozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G. D.Prendergast, Owen J. L. Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B.Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, MizuhoSakai, Hiroki Sato, Hironori Satoh, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Naoko Suzuki, Rolf K. Swoboda, Peter A. C.’t Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson, Hiroo Toyoda, TetsuroToyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E. Vorontsov, Wyeth W. Wasserman, Shoko Watanabe, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Emily J. Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Susan E. Zabierowski, Peter G. Zhang, XiaobeiZhao, Silvia Zucchelli, 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, Yoshihide Hayashizaki.
    Nature
    DOI: 10.1038/nature13182
  • An atlas of active enhancers across human cell types and tissues.

    Enhancers control the correct temporal and cell-type-specific activation of gene expression. We have made an atlas of active enhancers across the majority of human tissues and cell types. The atlas is used to compare regulatory programs between different cells, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers.

    Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki, Evgenia Ntini, Erik Arner, Eivind Valen, Kang Li, Lucia Schwarzfischer, Dagmar Glatz, Johanna Raithel, Berit Lilje, Nicolas Rapin, Frederik Otzen Bagger, Mette Jørgensen, Peter Refsing Andersen, Nicolas Bertin, Owen Rackham, A. Maxwell Burroughs, J. Kenneth Baillie, Yuri Ishizu, Yuri Shimizu, Erina Furuhata, Shiori Maeda, Yutaka Negishi, Christopher J. Mungall, Terrence F. Meehan, Timo Lassmann, Masayoshi Itoh, Hideya Kawaji, Naoto Kondo, Jun Kawai, Andreas Lennartsson, Carsten O. Daub, Peter Heutink, David A. Hume, Torben Heick Jensen, Harukazu Suzuki, Yoshihide Hayashizaki, Ferenc Müller, The FANTOM Consortium, Alistair R. R. Forrest, Piero Carninci, Michael Rehli & Albin Sandelin
    Nature
    DOI: 10.1038/nature12787
  • Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

    Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Our analysis suggests a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation.

    Erik Arner, Carsten O Daub, Kristoffer Vitting-Seerup, Robin Andersson, Berit Lilje, Finn Drablos, Andreas Lennartsson, Michelle Rönnerblad, Olga Hrydziuszko, Morana Vitezic, Tom C Freeman, Ahmad Alhendi, Peter Arner, Richard Axton, J Kenneth Baillie, Anthony Beckhouse, Beatrice Bodega, James Briggs, Frank Brombacher, Margaret Davis, Michael Detmar, Anna Ehrlund, Mitsuhiro Endoh, Afsaneh Eslami, Michela Fagiolini, Lynsey Fairbairn, Geoffrey J Faulkner, Carmelo Ferrai, Malcolm E Fisher, Lesley Forrester, Daniel Goldowitz, Reto Guler, Thomas Ha, Mitsuko Hara, Meenhard Herlyn, Tomokatsu Ikawa, Chieko Kai, Hiroshi Kawamoto, Levon Khachigian, Peter S Klinken, Soichi Kojima, Haruhiko Koseki, Sarah Klein, Niklas Mejhert, Ken Miyaguchi, Yosuke Mizuno, Mitsuru Morimoto, Kelly J Morris, Christine Mummery, Yutaka Nakachi, Soichi Ogishima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry Ovchinnikov, Robert Passier, Margaret Patrikakis, Ana Pombo, Xian-Yang Qin, Sugata Roy, Hiroki Sato, Suzana Savvi, Alka Saxena, Anita Schwegmann, Daisuke Sugiyama, Rolf Swoboda, Hiroshi Tanaka, Andru Tomoiu, Louise N Winteringham, Ernst Wolvetang, Chiyo Yanagi-Mizuochi, Misako Yoneda, Susan Zabierowski, Peter Zhang, Imad Abugessaisa, Nicolas Bertin, Alexander D. Diehl, Shiro Fukuda, Masaki Furuno, Jayson Harshbarger, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Yuri Ishizu, Masayoshi Itoh, Tsugumi Kawashima, Miki Kojima, Naoto Kondo, Marina Lizio, Terrence F. Meehan, Christopher J Mungall, Mitsuyoshi Murata, Hiromi Nishiyori-Sueki, Serkan Sahin, Sayako Sato-Nagao, Jessica Severin, Michiel JL de Hoon, Jun Kawai, Takeya Kasukawa, Timo Lassmann, Harukazu Suzuki, Hideya Kawaji, Kim M Summers, Christine Wells, FANTOM Consortium, David A Hume, Alistair RR Forrest, Albin Sandelin, Piero Carninci, Yoshihide Hayashizaki
    Science
    DOI: 10.1126/science.1259418
  • Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

    Alexandre Fort, Kosuke Hashimoto, Daisuke Yamada, Md Salimullah, Chaman A Keya, Alka Saxena, Alessandro Bonetti, Irina Voineagu, Nicolas Bertin, Anton Kratz, Yukihiko Noro, Chee-Hong Wong, Michiel de Hoon, Robin Andersson, Albin Sandelin, Harukazu Suzuki, Chia-Lin Wei, Haruhiko Koseki, The FANTOM Consortium, Yuki Hasegawa, Alistair R R Forrest & Piero Carninci
    Nature Genetics 2014
    DOI: 10.1038/ng.2965
  • FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

    Imad Abugessaisa, Hisashi Shimoji, Serkan Sahin, Atsushi Kondo, Jayson Harshbarger, Marina Lizio, Yoshihide Hayashizaki, Piero Carninci, The FANTOM consortium, Alistair Forrest, Takeya Kasukawa, and Hideya Kawaji
    Database 2016
    DOI: 10.1093/database/baw105
  • DeepCAGE transcriptomics identify HOXD10 as transcription factor regulating lymphatic endothelial responses to VEGF-C

    Sarah Klein, Lothar C. Dieterich, Anthony Mathelier, Chloé Chong, Adriana Sliwa-Primorac, Young-Kwon Hong, Jay W. Shin, Marina Lizio, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, the FANTOM consortium, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest, Wyeth W. Wasserman, Michael Detmar
    J Cell Sci 2016
    DOI: 10.1242/jcs.186767
  • DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium.

    Dieterich LC, Klein S, Mathelier A, Sliwa-Primorac A, Ma Q, Hong YK, Shin JW, Hamada M, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest AR, Wasserman WW, Detmar M.
    Cell Rep. 2015
    DOI: 10.1016/j.celrep.2015.10.002
  • Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line.

    Lizio M, Ishizu Y, Itoh M, Lassmann T, Hasegawa A, Kubosaki A, Severin J, Kawaji H, Nakamura Y; FANTOM consortium, Suzuki H, Hayashizaki Y, Carninci P, Forrest AR.
    Front Genet. 2015
    DOI: 10.3389/fgene.2015.00331
  • Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases

    Yasuhiro Murakawa, Masahito Yoshihara, Hideya Kawaji, Miki Nishikawa, Hatem Zayed, Harukazu Suzuki, FANTOM Consortium, Yoshihide Hayashizaki
    Trends in Genetics Volume 32, Issue 2, February 2016
    DOI: 10.1016/j.tig.2015.11.004
  • Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

    Georges St. Laurent, Yuri Vyatkin, Denis Antonets, Maxim Ri, Yao Qi, Olga Saik, Dmitry Shtokalo, Michiel J.L. de Hoon, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Erik Arner, Alistair R.R. Forrest, The FANTOM consortium, Estelle Nicolas, Timothy A. McCaffrey, Piero Carninci, Yoshihide Hayashizaki, Claes Wahlestedt, and Philipp Kapranov
    Nucl. Acids Res. 20 April 2016
    DOI: 10.1093/nar/gkw162
  • A predictive computational framework for direct reprogramming between human cell types

    Owen J L Rackham, Jaber Firas, Hai Fang, Matt E Oates, Melissa L Holmes, Anja S Knaupp, The FANTOM Consortium, Harukazu Suzuki, Christian M Nefzger, Carsten O Daub, Jay W Shin, Enrico Petretto, Alistair R R Forrest, Yoshihide Hayashizaki, Jose M Polo, Julian Gough
    Nature Genetics 2016
    DOI: 10.1038/ng.3487
  • A draft network of ligand-receptor-mediated multicellular signalling in human

    Jordan A Ramilowski, Tatyana Goldberg, Jayson Harshbarger, Edda Kloppman, Marina Lizio, Venkata P Satagopam, Masayoshi Itoh, Hideya Kawaji, Piero Carninci, Burkhard Rost, Alistair RR Forrest
    Nature communications 2015
    DOI: 10.1038/ncomms8866
  • Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

    Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T, Hayashizaki Y, Carninci P, Forrest AR; FANTOM5 Consortium.
    Cancer Res. 2016
    DOI: 10.1158/0008-5472.CAN-15-0484
  • The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

    Laurence D. Hurst, Avazeh T. Ghanbarian, Alistair R. R. Forrest, FANTOM consortium, Lukasz Huminiecki
    PLOS Bio. 2015
    DOI: 10.1371/journal.pbio.1002315
  • Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage

    Daniel Carbajo, Shigeyuki Magi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Erik Arner, Alistair R. R. Forrest, Piero Carninci, Yoshihide Hayashizaki, Carsten O. Daub, FANTOM consortium, Mariko Okada-Hatakeyama
    PLOS one 2015
    DOI: 10.1371/journal.pone.0144176
  • The frequent evolutionary birth and death of functional promoters in mouse and human

    Robert S Young, Yoshihide Hayashizaki, Robin Andersson, Albin Sandelin, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Piero Carninci, Wendy A Bickmore, Alistair R Forrest, Martin S Taylor, FANTOM Consortium
    Genome research
    DOI: 10.1101/gr.190546.115
  • Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells

    Marco Mina, Shigeyuki Magi, Giuseppe Jurman, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Erik Arner, Alistair RR Forrest, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub, Mariko Okada-Hatakeyama, Cesare Furlanello, FANTOM Consortium
    Scientific reports
    DOI: 10.1038/srep11999
  • EpiFactors: a comprehensive database of human epigenetic factors and complexes

    Yulia A. Medvedeva, Andreas Lennartsson, Rezvan Ehsani, Ivan V. Kulakovskiy, Ilya E. Vorontsov, Pouda Panahandeh, Grigory Khimulya, Takeya Kasukawa, The FANTOM Consortium and Finn Drabløs
    Database
    DOI: 10.1093/database/bav067
  • Transcription factor, promoter, and enhancer utilization in human myeloid cells

    Anagha Joshi, Christopher Pooley, Tom C. Freeman, Andreas Lennartsson, Magda Babina, Christian Schmidl, Teunis Geijtenbeek, the FANTOM Consortium, Tom Michoel, Jessica Severin, Masayoshi Itoh, Timo Lassmann, Hideya Kawaji, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, Michael Rehli and David A. Hume
    Journal of leukocyte biology
    DOI: 10.1189/jlb.6TA1014-477RR
  • Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells' differentiation in vitro and in neurochemical models of Parkinson's disease

    Claudia Carrieri, Alistair RR Forrest, Claudio Santoro, Francesca Persichetti, Piero Carninci, Silvia Zucchelli, Stefano Gustincich
    Frontiers in Cellular Neuroscience
    DOI: 10.3389/fncel.2015.00114
  • Paradigm shifts in genomics through the FANTOM projects

    Michiel de Hoon, Jay W Shin, Piero Carninci
    Mammalian Genome
    DOI: 10.1007/s00335-015-9593-8
  • CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

    Vanja Haberle, Alistair RR Forrest, Yoshihide Hayashizaki, Piero Carninci, Boris Lenhard
    Nucleic acids research
    DOI: 10.1093/nar/gkv054
  • CAGE-defined promoter regions of the genes implicated in Rett Syndrome

    Morana Vitezic, Nicolas Bertin, Robin Andersson, Leonard Lipovich, Hideya Kawaji, Timo Lassmann, Albin Sandelin, Peter Heutink, Dan Goldowitz, Thomas Ha, Peter Zhang, Annarita Patrizi, Michela Fagiolini, Alistair RR Forrest, Piero Carninci, Alka Saxena
    BMC genomics
    DOI: 10.1186/1471-2164-15-1177
  • Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium

    Nancy Yiu-Lin Yu, Björn M. Hallström, Linn Fagerberg, Fredrik Ponten, Hideya Kawaji, Piero Carninci, Alistair R. R. Forrest, The FANTOM Consortium, Yoshihide Hayashizaki, Mathias Uhlén and Carsten O. Daub
    Nucleic Acids Research 2015
    DOI: 10.1093/nar/gkv608
  • Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics

    Sugata Roy, Sebastian Schmeier, Erik Arner, Tanvir Alam, Suraj P. Parihar, Mumin Ozturk, Ousman Tamgue, Hideya Kawaji, Michiel J. L. de Hoon, Masayoshi Itoh1, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest, Vladimir B. Bajic, Reto Guler, FANTOM Consortium, Frank Brombacher, and Harukazu Suzuki
    Nucleic Acids Research 2015
    DOI: 10.1093/nar/gkv646
  • Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response.

    Aitken S, Magi S, Alhendi AM, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Forrest AR, Hayashizaki Y; FANTOM Consortium, Khachigian LM, Okada-Hatakeyama M, Semple CA.
    PLoS Comput Biol.
    DOI: 10.1371/journal.pcbi.1004217
  • Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body

    Masahito Yoshihara, Hiroko Ohmiya, Susumu Hara, Satoshi Kawasaki, FANTOM consortium , Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji , Motokazu Tsujikawa, Kohji Nishida
    PLoS ONE
    DOI: 10.1371/journal.pone.0117581
  • Gateways to the FANTOM5 promoter level mammalian expression atlas

    Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda1, Fumi Hori, Sachi Ishikawa-Kato, Christopher J Mungall, Erik Arner, J Kenneth Baillie, Nicolas Bertin, Hidemasa Bono, Michiel de Hoon, Alexander D Diehl, Emmanuel Dimont, Tom C Freeman, Kaori Fujieda, Winston Hide, Rajaram Kaliyaperumal, Toshiaki Katayama, Timo Lassmann, Terrence F Meehan, Koro Nishikata, Hiromasa Ono, Michael Rehli, Albin Sandelin, Erik A Schultes, Peter AC ‘t Hoen, Zuotian Tatum, Mark Thompson, Tetsuro Toyoda, Derek W Wright, Carsten O Daub, Masayoshi Itoh, Piero Carninci, Yoshihide Hayashizaki, Alistair RR Forrest, Hideya Kawaji and the FANTOM consortium
    Genome Biology
    DOI: 10.1186/s13059-014-0560-6
  • The Statistical Geometry of Transcriptome Divergence in Cell Type Evolution and Cancer

    Cong Liang, the FANTOM Consortium, Alistair R. R. Forrest & Günter P. Wagner
    Nature Communications 2015, 6:6066
    DOI: 10.1038/ncomms7066
  • A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators.

    Laurence D Hurst, Oxana Sachenkova, Carsten Daub, Alistair R. R. Forrest and Lukasz Huminiecki
    Genome Biology 2014, 15:413
    DOI: 10.1186/s13059-014-0413-3
  • Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules

    Alice Grison, Silvia Zucchelli, Alice Urzì, Ilaria Zamparo, Dejan Lazarevic, Giovanni Pascarella, Paola Roncaglia, Alejandro Giorgetti, Paula Garcia-Esparcia, Christina Vlachouli, Roberto Simone, Francesca Persichetti, Alistair RR Forrest, Yoshihide Hayashizaki, Paolo Carloni, Isidro Ferrer, Claudia Lodovichi, Charles Plessy, the FANTOM Consortium, Piero Carninci and Stefano Gustincich
    BMC Genomics 2014, 15:729
    DOI: 10.1186/1471-2164-15-729
  • Deep sequencing blood transcriptomes

    Alistair R.R. Forrest
    Blood 123 (17)
    DOI: 10.1182/blood-2014-03-563452
  • Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer

    Roberto Verardo, Silvano Piazza, Enio Klaric, Yari Ciani, Giulio Bussadori, Stefania Marzinotto, Laura Mariuzzi, Daniela Cesselli, Antonio P. Beltrami, Miguel Mano, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, the FANTOM consortium, Carlo A. Beltrami and Claudio Schneider
    Stem Cells
    DOI: 10.1002/stem.1791
  • CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes

    Yuki Hasegawa, Dave Tang, Naoko Takahashi, Yoshihide Hayashizaki, Alistair R. R. Forrest, the FANTOM consortium and Harukazu Suzuki
    Scientific Reports
    DOI: 10.1038/srep05228
  • A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation

    Yasuhiro Tomaru, Ryota Hasegawa, Takahiro Suzuki, Taiji Sato, Atsutaka Kubosaki, Masanori Suzuki, Hideya Kawaji, Alistair R.R. Forrest, Yoshihide Hayashizaki, FANTOM Consortium, Jay W. Shin, and Harukazu Suzuki
    Nucleic Acids Research 2014
    DOI: 10.1093/nar/gku567
  • RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE)

    Hiroko Ohmiya, Morana Vitezic1, Martin C Frith, Masayoshi Itoh, Piero Carninci, Alistair RR Forrest, Yoshihide Hayashizaki, Timo Lassmann and The FANTOM Consortium
    BMC Genomics 2014, 15:269
    DOI: 10.1186/1471-2164-15-269
  • Redefinition of the human mast cell transcriptome by deep sequencing.

    Using freshly isolated skin-derived Mast cells (MCs) FANTOM5 reveals a comprehensive view of the human MC transcriptome. Mast cells are unique in the hematopoietic lineage and are only distantly related to basophils. We also show that mast cells express BMP receptors and that BMPs can promote survival and recovery to stimulation of human MCs.

    Efthymios Motakis, Sven Guhl, Yuri Ishizu, Masayoshi Itoh, Hideya Kawaji, Michiel de Hoon, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Torsten Zuberbier, Alistair R R Forrest, Magda Babina, and the FANTOM consortium
    Blood
    DOI: 10.1182/blood-2013-02-483792
  • Transcription and enhancer profiling in human monocyte subsets.

    Complementary CAGE and epigenetic profiling dissects differences between the three major subpopulations of human monocytes. This FANTOM5 study highlights differential gene, transcription factor and enhancer usage and identifies previously unrecognized metabolic differences between subpopulations.

    Christian Schmidl, Kathrin Renner, Katrin Peter, Ruediger Eder, Timo Lassmann, Piotr J. Balwierz, Masayoshi Itoh, Sayaka Nago-Sato, Hideya Kawaji, Piero Carninci, Harukazu Suzuki, Yoshihide Hayashizaki, Reinhard Andreesen, David A. Hume, Petra Hoffmann, Alistair R. R. Forrest, Marina P. Kreutz, Matthias Edinger, Michael Rehli for the FANTOM consortium
    Blood
    DOI: 10.1182/blood-2013-02-484188
  • The enhancer and promoter landscape of human regulatory and conventional T cell subpopulations.

    Their ability to avert immune reactions makes regulatory T cells (Treg) highly interesting for clinical application. This FANTOM5 study investigates transcription factor networks in naïve and memory Treg and their conventional T cell (Tconv) counterparts both before and after in vitro expansion and shows that in vitro expanded Treg do not dramatically change their Treg-specific effector molecule repertoire.

    Christian Schmid, Leo Hansmann, Timo Lassmann, Piotr J. Balwierz, Hideya Kawaji, Masayoshi Itoh, Jun Kawai, Sayaka Nagao-Sato, Harukazu Suzuki, Reinhard Andreesen, Yoshihide Hayashizaki, Alistair R. R. Forrest, Piero Carninci, Petra Hoffmann, Matthias Edinger, Michael Rehli, for the FANTOM consortium
    Blood
    DOI: 10.1182/blood-2013-02-486944
  • Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation

    Overall this study depicts in detail the epigenetic and transcriptional changes that occur during granulopoiesis and supports the role of DNA methylation as a regulatory mechanism in blood cell differentiation. We show that methylation change at specific differentiation stages and overlap with the activity of key hematopoietic transcription factors. Also, differentially methylated sites were overrepresented in enhancer elements and enriched in enhancers that become active during differentiation.

    Michelle Rönnerblad, Robin Andersson, Tor Olofsson, Iyadh Douag, Mohsen Karimi, Sören Lehmann, Ilka Hoof, Michiel de Hoon, Masayohi Itoh, Sayaka Nago-Sato, Hideya Kawaji, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Albin Sandelin, Karl Ekwall, Erik Arner, Andreas Lennartsson and the FANTOM consortium
    Blood
    DOI: 10.1182/blood-2013-02-482893
  • High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis

    Hematopoietic differentiation is governed by a complex regulatory program controlling the generation of different lineages of blood cells from multipotent hematopoietic stem cells. The transcriptional program that dictates hematopoietic cell fate and differentiation requires an epigenetic memory function provided by a network of epigenetic factors regulating DNA methylation, posttranslational histone modifications, and chromatin structure. To elucidate the contributions of different epigenetic factors in human hematopoiesis, high-throughput cap analysis of gene expression was used to build transcription profiles of 199 epigenetic factors in a wide range of blood cells.

    Punit Prasad, Michelle Rönnerblad, Erik Arner, Masayohi Itoh, Hideya Kawaji, Timo Lassmann, Carsten Daub, Alistair R.R. Forrest, Andreas Lennartsson, Karl Ekwall, and the FANTOM consortium
    Blood
    DOI: 10.1182/blood-2013-02-483537
  • Comparison of CAGE and RNA-seq transcriptome profiling using a clonally amplified and single molecule next generation sequencing

    We compared CAGE using both 2nd and 3rd generation sequencers and RNA-seq using a 2nd generation sequencer based on a panel of RNA mixtures from two human cell lines to examine power in discrimination of biological states, detection of differentially expressed genes, linearity of measurements as well as quantification reproducibility. The result provides a perspective on performance of these platforms, which will be a baseline to design further experiments to tackle complex transcriptomes uncovered in a wide range of cell types.

    Hideya Kawaji, Marina Lizio, Masayoshi Itoh, Mutsumi Kanamori-Katayama, Ai Kaiho, Hiromi Nishiyori-Sueki, Jay Shin, Miki Kojima-Ishiyama, Mitsuoki Kawano, Mitsuyoshi Murata, Noriko Ninomiya-Fukuda, Sachi Ishikawa-Kato, Sayaka Nagao-Sato, Shohei Noma, Yoshihide Hayashizaki, Alistair R.R. Forrest, Piero Carninci, and the FANTOM consortium
    Genome Research
    DOI: 10.1101/gr.156232.113
  • Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.

    Regulatory T (Treg) cells, which specifically express the transcription factor Foxp3, are engaged in the maintenance of immunological self-tolerance and homeostasis. Analysis of FANTOM5 CAGE data with epigenome data including DNA methylation and Transcription factor binding sites reveals that Treg specific demethylation and Foxp3 appear to play distinct but complementary roles in Treg specific gene regulation.

    Hiromasa Morikawa, Naganari Ohkura, Alexis Vandenbon, Masayohi Itoh, Sayaka Nago-Sato, Hideya Kawaji, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Daron Standley, Hiroshi Date, Shimon Sakaguchi, and the FANTOM consortium
    Proc Natl Acad Sci USA.
    DOI: 10.1073/pnas.1312717110
  • The Evolution of Human Cells in terms of Protein Innovation

    Combining FANTOM5 CAGE data and protein domain annotation we are able to get a view on how different cell types have evolved. We are able to identify known evolutionary events as well highlight other novel events that until know have remained undetected.

    Adam J. Sardar, Matt E. Oates, Hai Fang, Alistair R.R. Forrest, Hideya Kawaji, The FANTOM Consortium, Julian Gough, and Owen J.L. Rackham
    Molecular Biology and Evolution
    DOI: 10.1093/molbev/mst139
  • Interactive visualization and analysis of large-scale NGS data-sets using ZENBU.

    Next generation sequencing protocols such as RNA-seq, ChIP-seq, DHS-seq and CAGE across large sample collections are generating a wealth of data to elucidate genomic function. To facilitate interactive comparison of results across 1000s of NGS experiments we present ZENBU, a web application combining data integration, and data analysis into a genome browser with enhanced gene expression and epigenomic visualization capabilities.

    Jessica Severin, Marina Lizio, Jayson Harshbarger, Hideya Kawaji, Carsten O Daub, Yoshihide Hayashizaki, The FANTOM Consortium, Nicolas Bertin, Alistair R R Forrest
    Nature Biotechnology 32, 217–219 (2014)
    DOI: 10.1038/nbt.2840
  • Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions.

    The fibrillins and latent transforming growth factor binding proteins (LTBPs) form a superfamily of proteins involved in the structure of the extracellular matrix and in controlling the bioavailability of TGFβ family members. We present a study of transcription start sites, which suggests this important class of extracellular matrix proteins is subject to subtle regulatory variations that explain the differential roles of members of this gene family.

    Margaret R Davis, Robin Andersson, Jessica Severin, Michiel de Hoon, Nicolas Bertin, J Kenneth Baillie, Hideya Kawaji, Albin Sandelin, Alistair RR Forrest, Kim M Summers
    Molecular Genetics and Metabolism
    DOI: 10.1016/j.ymgme.2013.12.006
  • Explaining the correlations among properties of mammalian promoters

    Promoters have mysterious variation in CpG richness, TATA signals, evolutionary conservation, expression specificity, and chromosomal spread of transcription start sites. We warn of biases in measuring these properties, show that most promoters have rather non-specific expression, and provide simple explanations for the correlations among the properties.

    Martin C. Frith and the FANTOM consortium
    Nucleic Acids Research
    DOI: 10.1093/nar/gku115
  • CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments.

    CAGExploreR is an R package that facilitates the detection and visualization of changes in the relative transcription from promoter regions in multi-promoter genes, all in the context of overall gene expression. Multiple samples can be compared simultaneously. Primarily based on the FANTOM5 promoter set definitions, however other regions such as MPromDb or user-supplied regions can also be used.

    Emmanuel Dimont, Oliver Hofmann, Alistair R. R. Forrest, Hideya Kawaji, the FANTOM Consortium, and Winston Hide
    Bioinformatics
    DOI: 10.1093/bioinformatics/btu125
  • Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells

    Obesity confers an increased risk of developing specific cancer forms. Increased fat cell secretion of adipokines may promote malignant tumors in obesity via tissue cross-talk. We found ceruloplasmin (CP) expression to be strongly enriched in obesity-associated cancer, and in adipose tissue of obese subjects. We demonstrate that CP is a novel adipokine, with increased production and secretion in obesity.

    Erik Arner, Alistair R R Forrest, Anna Ehrlund, Niklas Mejhert, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Jurga Laurencikiene, Mikael Rydé, Peter Arner, and the FANTOM consortium.
    PLOS ONE
    DOI: 10.1371/journal.pone.0080274
  • Effects of cytosine methylation on transcription factor binding sites

    Methylation of 16% of individual CpGs negatively correlates with neighboring TSS expression. We observed a selection against these CpGs within transcription factor binding sites (TFBSs), being stronger for repressors than for activators, as well as for core TFBS positions than for flanking ones. We suggested that selective methylation of TFBSs preventing transcription factor binding is restricted to special cases and cannot be a global mechanism for transcription regulation.

    Yulia A Medvedeva, Abdullah Khamis, Ivan V Kulakovskiy, Wail Ba-Alawi, Md Shariful I Bhuyan, Hideya Kawaji, Timo Lassmann, Matthias Harbers, Alistair RR Forrest, Vladimir B Bajic and the FANTOM consortium
    BMC genomics
    DOI: 10.1186/1471-2164-15-119
  • Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines

    Deciphering the most common modes by which chromatin regulates transcription is an important task for improving our understanding of human cellular biology. Transcriptional data from FANTOM5 is integrated data from the ENCODE project to characterize chromatin features around expressed and repressed transcription start sites in four human cell lines.

    Morten Rye, Geir K Sandve, Carsten O Daub, Hideya Kawaji, Piero Carninci, Alistair RR Forrest, Finn Drabløs
    BMC Genomics
    DOI: 10.1186/1471-2164-15-120
  • Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer

    Masayoshi Itoh, Miki Kojima, Sayaka Nagao-Sato, Eri Saijo, Timo Lassmann, Mutsumi Kanamori-Katayama, Ai Kaiho, Marina Lizio, Hideya Kawaji, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki
    PLoS One 7(1):e30809 (2012)
    PUBMED: 22303458; DOI: 10.1371/journal.pone.0030809
  • Unamplified Cap Analysis of Gene Expression on a single molecule sequencer

    Mutsumi Kanamori-Katayama, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Shintaro Katayama, Miki Kojima, Nicolas Bertin, Ai Kaiho, Noriko Ninomiya, Carsten O. Daub, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki.
    Genome Research 21, 1150-9 (2011)
    PUBMED: 21596820; DOI: 10.1101/gr.115469.110
  • Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

    Charles Plessy, Nicolas Bertin, Hazuki Takahashi, Roberto Simone, Md Salimullah, Timo Lassmann, Morana Vitezic, Jessica Severin, Signe Olivarius, Dejan Lazarevic, Nadine Hornig, Valerio Orlando, Ian Bell, Hui Gao, Jacqueline Dumais, Philipp Kapranov, Huaien Wang, Carrie A Davis, Thomas R Gingeras, Jun Kawai, Carsten O Daub, Yoshihide Hayashizaki, Stefano Gustincich, Piero Carninci
    Nature Methods 7, 528–34 (2010)
    PUBMED: 20543846; DOI: 10.1038/nmeth.1470
  • NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes

    Md Salimullah, Sakai Mizuho, Charles Plessy, Piero Carninci
    Cold Spring Harbor Protocols, (2011)
    PUBMED: 21205859; DOI: 10.1101/pdb.prot5559

FANTOM4 Papers

  • An atlas of combinatorial transcriptional regulation in mouse and man

    Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kawaji H, Kubosaki A, Lassmann T, van Nimweg en E, Ogawa C, Teasdale RD, Tegnr J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitaz ume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y.
    Cell 140, 744-52 (2010)
    PUBMED: 20211142; DOI: 10.1016/j.cell.2010.01.044
  • The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

    Suzuki H, Forrest ARR, Van Nimwegen E, Daub CO, Balwierz P, Irvine K, Lassman T, Ravasi T, Hasegawa Y, de Hoon M, Katayama S, Schroder K, Carninci P, Akalin A, Ando Y, Arner E, Asada M, Asahra H, Bailey T, Bajic V B, Bauer D, Beckhouse A, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk A M, Chiba J, Cloonan N, Dawe A, Dostie J, Engstrom P G, Essack M, Faulkner G J, Fink J, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond S, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, MacPherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin S, Schmeier S, Scho¨nbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St. Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegne´r J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y.
    Nature Genetics 41, 553-562 (2009)
    PUBMED: 19377474; DOI: 10.1038/ng.375
  • Tiny RNAs associated with transcription start sites in animals

    Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest ARR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V,Carninci P, Hayashizaki Y, Mattick JS.
    Nature Genetics 41, 572-578 (2009)
    PUBMED: 19377478; DOI: 10.1038/ng.312
  • The regulated retrotransposon transcriptome of mammalian cells

    Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest ARR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P.
    Nature Genetics 41, 563-571 (2009)
    PUBMED: 19377475, DOI: 10.1038/ng.368
  • Click here to see FANTOM4 satellite papers

FANTOM3 Papers

  • Genome-wide analysis of mammalian promoter architecture and evolution

    Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y.
    Nature Genetics 38, 626-635 (2006)
    PUBMED: 16645617, DOI: 10.1038/ng1789
  • The transcriptional landscape of the mammalian genome

    Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y.
    Science 309, 1559-1563 (2005)
    PUBMED: 16141072, DOI: 10.1126/science.1112014
  • Antisense transcription in the mammalian transcriptome

    Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engstrom PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C.
    Science 309, 1564-1566 (2005)
    PUBMED: 16141073, DOI: 10.1126/science.1112009
  • Click here to see FANTOM3 related papers

FANTOM2 Papers

  • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

    Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team.
    Nature 420, 563-73 (2002)
    PUBMED: 12466851, DOI: 10.1038/nature01266
  • Click here to see FANTOM2 satellite papers

FANTOM1 Papers

  • Functional annotation of a full-length mouse cDNA collection

    Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schönbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y; RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium.
    Nature 409, 685-90 (2001)
    PUBMED: 11217851, DOI: 10.1038/35055500