Gateways to the FANTOM5 promoter level mammalian expression atlas

Marina Lizio; Jayson Harshbarger; Hisashi Shimoji; Jessica Severin; Takeya Kasukawa; Serkan Sahin; Imad Abugessaisa; Shiro Fukuda; 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 Gustav Sandelin; Erik A Schultes; Peter A C 't Hoen; Zuotian Tatum; Mark Thompson; Tetsuro Toyoda; Derek W Wright; Carsten O Daub; Masayoshi Itoh; Piero Carninci; Yoshihide Hayashizaki; Alistair R R Forrest; Hideya Kawaji

doi:10.1186/s13059-014-0560-6

Gateways to the FANTOM5 promoter level mammalian expression atlas

Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda, 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 FujiedaWinston Hide, Rajaram Kaliyaperumal, Toshiaki Katayama, Timo Lassmann, Terrence F Meehan, Koro Nishikata, Hiromasa Ono, Michael Rehli, Albin Gustav Sandelin, Erik A Schultes, Peter A C 't Hoen, Zuotian Tatum, Mark Thompson, Tetsuro Toyoda, Derek W Wright, Carsten O Daub, Masayoshi Itoh, Piero Carninci, Yoshihide Hayashizaki, Alistair R R Forrest, Hideya Kawaji

Bioinformatik og RNA Biologi

319 Citationer (Scopus)

561 Downloads (Pure)

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/). 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.

Originalsprog	Engelsk
Artikelnummer	22
Tidsskrift	Genome Biology (Online Edition)
Vol/bind	16
Antal sider	14
ISSN	1474-7596
DOI	https://doi.org/10.1186/s13059-014-0560-6
Status	Udgivet - 5 jan. 2015

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10.1186/s13059-014-0560-6Licens: CC BY

Gateways to the FANTOM5 promoter level mammalian expression atlasForlagets udgivne version, 2,64 MBLicens: CC BY

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Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S., Mungall, C. J., Arner, E., Baillie, J. K., Bertin, N., Bono, H., de Hoon, M., Diehl, A. D., Dimont, E., Freeman, T. C., ... Kawaji, H. (2015). Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biology (Online Edition), 16, [22]. https://doi.org/10.1186/s13059-014-0560-6

Lizio, M, Harshbarger, J, Shimoji, H, Severin, J, Kasukawa, T, Sahin, S, Abugessaisa, I, Fukuda, S, Hori, F, Ishikawa-Kato, S, Mungall, CJ, Arner, E, Baillie, JK, Bertin, N, Bono, H, de Hoon, M, Diehl, AD, Dimont, E, Freeman, TC, Fujieda, K, Hide, W, Kaliyaperumal, R, Katayama, T, Lassmann, T, Meehan, TF, Nishikata, K, Ono, H, Rehli, M, Sandelin, AG, Schultes, EA, 't Hoen, PAC, Tatum, Z, Thompson, M, Toyoda, T, Wright, DW, Daub, CO, Itoh, M, Carninci, P, Hayashizaki, Y, Forrest, ARR & Kawaji, H 2015, 'Gateways to the FANTOM5 promoter level mammalian expression atlas', Genome Biology (Online Edition), bind 16, 22. https://doi.org/10.1186/s13059-014-0560-6

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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/). 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.",

author = "Marina Lizio and Jayson Harshbarger and Hisashi Shimoji and Jessica Severin and Takeya Kasukawa and Serkan Sahin and Imad Abugessaisa and Shiro Fukuda and Fumi Hori and Sachi Ishikawa-Kato and Mungall, {Christopher J} and Erik Arner and Baillie, {J Kenneth} and Nicolas Bertin and Hidemasa Bono and {de Hoon}, Michiel and Diehl, {Alexander D} and Emmanuel Dimont and Freeman, {Tom C} and Kaori Fujieda and Winston Hide and Rajaram Kaliyaperumal and Toshiaki Katayama and Timo Lassmann and Meehan, {Terrence F} and Koro Nishikata and Hiromasa Ono and Michael Rehli and Sandelin, {Albin Gustav} and Schultes, {Erik A} and {'t Hoen}, {Peter A C} and Zuotian Tatum and Mark Thompson and Tetsuro Toyoda and Wright, {Derek W} and Daub, {Carsten O} and Masayoshi Itoh and Piero Carninci and Yoshihide Hayashizaki and Forrest, {Alistair R R} and Hideya Kawaji",

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T1 - Gateways to the FANTOM5 promoter level mammalian expression atlas

AU - Lizio, Marina

AU - Harshbarger, Jayson

AU - Shimoji, Hisashi

AU - Severin, Jessica

AU - Kasukawa, Takeya

AU - Sahin, Serkan

AU - Abugessaisa, Imad

AU - Fukuda, Shiro

AU - Hori, Fumi

AU - Ishikawa-Kato, Sachi

AU - Mungall, Christopher J

AU - Arner, Erik

AU - Baillie, J Kenneth

AU - Bertin, Nicolas

AU - Bono, Hidemasa

AU - de Hoon, Michiel

AU - Diehl, Alexander D

AU - Dimont, Emmanuel

AU - Freeman, Tom C

AU - Fujieda, Kaori

AU - Hide, Winston

AU - Kaliyaperumal, Rajaram

AU - Katayama, Toshiaki

AU - Lassmann, Timo

AU - Meehan, Terrence F

AU - Nishikata, Koro

AU - Ono, Hiromasa

AU - Rehli, Michael

AU - Sandelin, Albin Gustav

AU - Schultes, Erik A

AU - 't Hoen, Peter A C

AU - Tatum, Zuotian

AU - Thompson, Mark

AU - Toyoda, Tetsuro

AU - Wright, Derek W

AU - Daub, Carsten O

AU - Itoh, Masayoshi

AU - Carninci, Piero

AU - Hayashizaki, Yoshihide

AU - Forrest, Alistair R R

AU - Kawaji, Hideya

PY - 2015/1/5

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N2 - 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/). 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.

AB - 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/). 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.

U2 - 10.1186/s13059-014-0560-6

DO - 10.1186/s13059-014-0560-6

M3 - Journal article

C2 - 25723102

SN - 1474-7596

VL - 16

JO - Genome Biology (Online Edition)

JF - Genome Biology (Online Edition)

M1 - 22

ER -

Gateways to the FANTOM5 promoter level mammalian expression atlas

Abstract

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