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Title: Gateways to the FANTOM5 promoter level mammalian expression atlas

Abstract

The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). In conclusion, this resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas.

Authors:
 [1];  [1];  [1];  [1];  [2];  [1];  [2];  [3];  [1];  [1];  [4];  [1];  [5];  [6];  [7];  [1];  [8];  [9];  [5];  [7] more »;  [10];  [11];  [7];  [12];  [13];  [14];  [7];  [15];  [16];  [17];  [11];  [11];  [11];  [14];  [5];  [3];  [18];  [1];  [19];  [1];  [20] « less
  1. RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan)
  2. RIKEN Center for Life Science Technologie, Kanagawa (Japan)
  3. RIKEN Yokohama Institute, Kanagawa (Japan)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. Univ. of Edinburgh, Scotland (United Kingdom)
  6. RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan); National Univ. of Singapore (Singapore)
  7. Research Organization of Information Systems, Chiba (Japan)
  8. Univ. at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY (United States)
  9. Harvard School of Public Health, Boston, MA (United States)
  10. Harvard School of Public Health, Boston, MA (United States); Univ. of Sheffield, Sheffield (United Kingdom)
  11. Leiden Univ. Medical Center, Leiden (Netherlands)
  12. RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan); The Univ. of Western Australia, Western Australia (Australia)
  13. European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge (United Kingdom)
  14. RIKEN Advanced Center for Computing and Communication, Saitama (Japan)
  15. Univ. Hospital Regensburg, Regensburg (Germany)
  16. Copenhagen Univ., Copenhagen (Denmark)
  17. Leiden Univ. Medical Center, Leiden (Netherlands); Leiden Univ., Leiden (Netherlands)
  18. RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan); RIKEN Preventive Medicine and Diagnosis Innovative Program, Saitama (Japan)
  19. RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Preventive Medicine and Diagnosis Innovative Program, Saitama (Japan)
  20. RIKEN Yokohama Institute, Kanagawa (Japan); RIKEN Center for Life Science Technologie, Kanagawa (Japan); RIKEN Preventive Medicine and Diagnosis Innovative Program, Saitama (Japan); RIKEN Advanced Center for Computing and Communication, Saitama (Japan)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Contributing Org.:
The FANTOM consortium
OSTI Identifier:
1256488
Grant/Contract Number:
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Genome Biology
Additional Journal Information:
Journal Volume: 16; Journal Issue: 1; Journal ID: ISSN 1465-6906
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING

Citation Formats

Lizio, Marina, Harshbarger, Jayson, Shimoji, Hisashi, Severin, Jessica, Kasukawa, Takeya, Sahin, Serkan, Abugessaisa, Imad, Fukuda, Shiro, Hori, Fumi, Ishikawa-Kato, Sachi, Mungall, Christopher J., Arner, Erik, Baillie, J. Kenneth, Bertin, Nicolas, Bono, Hidemasa, de Hoon, Michiel, Diehl, Alexander D., Dimont, Emmanuel, Freeman, Tom C., Fujieda, Kaori, Hide, Winston, Kaliyaperumal, Rajaram, Katayama, Toshiaki, Lassmann, Timo, Meehan, Terrence F., Nishikata, Koro, Ono, Hiromasa, Rehli, Michael, Sandelin, Albin, Schultes, Erik A., ‘t Hoen, Peter A. C., Tatum, Zuotian, Thompson, Mark, Toyoda, Tetsuro, Wright, Derek W., Daub, Carsten O., Itoh, Masayoshi, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., and Kawaji, Hideya. Gateways to the FANTOM5 promoter level mammalian expression atlas. United States: N. p., 2015. Web. doi:10.1186/s13059-014-0560-6.
Lizio, Marina, Harshbarger, Jayson, Shimoji, Hisashi, Severin, Jessica, Kasukawa, Takeya, Sahin, Serkan, Abugessaisa, Imad, Fukuda, Shiro, Hori, Fumi, Ishikawa-Kato, Sachi, Mungall, Christopher J., Arner, Erik, Baillie, J. Kenneth, Bertin, Nicolas, Bono, Hidemasa, de Hoon, Michiel, Diehl, Alexander D., Dimont, Emmanuel, Freeman, Tom C., Fujieda, Kaori, Hide, Winston, Kaliyaperumal, Rajaram, Katayama, Toshiaki, Lassmann, Timo, Meehan, Terrence F., Nishikata, Koro, Ono, Hiromasa, Rehli, Michael, Sandelin, Albin, Schultes, Erik A., ‘t Hoen, Peter A. C., Tatum, Zuotian, Thompson, Mark, Toyoda, Tetsuro, Wright, Derek W., Daub, Carsten O., Itoh, Masayoshi, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., & Kawaji, Hideya. Gateways to the FANTOM5 promoter level mammalian expression atlas. United States. doi:10.1186/s13059-014-0560-6.
Lizio, Marina, Harshbarger, Jayson, Shimoji, Hisashi, Severin, Jessica, Kasukawa, Takeya, Sahin, Serkan, Abugessaisa, Imad, Fukuda, Shiro, Hori, Fumi, Ishikawa-Kato, Sachi, Mungall, Christopher J., Arner, Erik, Baillie, J. Kenneth, Bertin, Nicolas, Bono, Hidemasa, de Hoon, Michiel, Diehl, Alexander D., Dimont, Emmanuel, Freeman, Tom C., Fujieda, Kaori, Hide, Winston, Kaliyaperumal, Rajaram, Katayama, Toshiaki, Lassmann, Timo, Meehan, Terrence F., Nishikata, Koro, Ono, Hiromasa, Rehli, Michael, Sandelin, Albin, Schultes, Erik A., ‘t Hoen, Peter A. C., Tatum, Zuotian, Thompson, Mark, Toyoda, Tetsuro, Wright, Derek W., Daub, Carsten O., Itoh, Masayoshi, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., and Kawaji, Hideya. Mon . "Gateways to the FANTOM5 promoter level mammalian expression atlas". United States. doi:10.1186/s13059-014-0560-6. https://www.osti.gov/servlets/purl/1256488.
@article{osti_1256488,
title = {Gateways to the FANTOM5 promoter level mammalian expression atlas},
author = {Lizio, Marina and Harshbarger, Jayson and Shimoji, Hisashi and Severin, Jessica and Kasukawa, Takeya and Sahin, Serkan and Abugessaisa, Imad and Fukuda, Shiro and Hori, Fumi and Ishikawa-Kato, Sachi and Mungall, Christopher J. and Arner, Erik and Baillie, J. Kenneth and Bertin, Nicolas and Bono, Hidemasa and de Hoon, Michiel and Diehl, Alexander D. and Dimont, Emmanuel and Freeman, Tom C. and Fujieda, Kaori and Hide, Winston and Kaliyaperumal, Rajaram and Katayama, Toshiaki and Lassmann, Timo and Meehan, Terrence F. and Nishikata, Koro and Ono, Hiromasa and Rehli, Michael and Sandelin, Albin and Schultes, Erik A. and ‘t Hoen, Peter A. C. and Tatum, Zuotian and Thompson, Mark and Toyoda, Tetsuro and Wright, Derek W. and Daub, Carsten O. and Itoh, Masayoshi and Carninci, Piero and Hayashizaki, Yoshihide and Forrest, Alistair R. R. and Kawaji, Hideya},
abstractNote = {The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE. Based on manual curation of sample information and development of an ontology for sample classification, we assemble the resulting data into a centralized data resource (http://fantom.gsc.riken.jp/5/). In conclusion, this resource contains web-based tools and data-access points for the research community to search and extract data related to samples, genes, promoter activities, transcription factors and enhancers across the FANTOM5 atlas.},
doi = {10.1186/s13059-014-0560-6},
journal = {Genome Biology},
number = 1,
volume = 16,
place = {United States},
year = {Mon Jan 05 00:00:00 EST 2015},
month = {Mon Jan 05 00:00:00 EST 2015}
}

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