Gateways to the FANTOM5 promoter level mammalian expression atlas

FANTOM Consortium; 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 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

FANTOM Consortium, 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. FreemanKaori Fujieda, Winston Hide, Rajaram Kaliyaperumal, Toshiaki Katayama, Timo Lassmann, Terrence F. Meehan, Koro Nishikata, Hiromasa Ono, Michael Rehli, Albin 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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

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.

Original language	English
Article number	22
Number of pages	14
Journal	Genome Biology
Volume	16
DOIs	https://doi.org/10.1186/s13059-014-0560-6
Publication status	Published - 5 Jan 2015

Keywords / Materials (for Non-textual outputs)

ANALYSIS GENE-EXPRESSION
CAP-ANALYSIS
TRANSCRIPTIONAL LANDSCAPE
FUNCTIONAL ANNOTATION
NATIONAL CENTER
HUMAN GENOME
RNA-SEQ
DATABASE
ONTOLOGIES
MOUSE

Access to Document

10.1186/s13059-014-0560-6

Gateways to the FANTOM5 promoter level mammalian expression atlas
© 2015 Lizio et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Final published version, 2.64 MBLicence: Creative Commons: Attribution (CC-BY)

http://genomebiology.com/2015/16/1/22

Biolayout Express3d: a community resource for the network visulisation and analysis of biological data and pathways
Freeman, T. & Enright, A. J.
BBSRC
1/07/10 → 29/11/13
Project: Research

Cite this

FANTOM Consortium, 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., ... Kawaji, H. (2015). Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biology, 16, Article 22. https://doi.org/10.1186/s13059-014-0560-6

@article{3a44175e06484500910d993e04e2a5b4,

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/). 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.",

keywords = "ANALYSIS GENE-EXPRESSION, CAP-ANALYSIS, TRANSCRIPTIONAL LANDSCAPE, FUNCTIONAL ANNOTATION, NATIONAL CENTER, HUMAN GENOME, RNA-SEQ, DATABASE, ONTOLOGIES, MOUSE",

author = "{FANTOM Consortium} and 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 Albin Sandelin and Schultes, {Erik A.} and Hoen, {Peter A. C't} 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",

year = "2015",

month = jan,

day = "5",

doi = "10.1186/s13059-014-0560-6",

language = "English",

volume = "16",

journal = "Genome Biology",

issn = "1465-6906",

publisher = "BioMed Central",

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FANTOM Consortium, 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, A, Schultes, EA, 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, vol. 16, 22. https://doi.org/10.1186/s13059-014-0560-6

TY - JOUR

T1 - Gateways to the FANTOM5 promoter level mammalian expression atlas

AU - FANTOM Consortium

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

AU - Schultes, Erik A.

AU - Hoen, Peter A. C't

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

Y1 - 2015/1/5

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.

KW - ANALYSIS GENE-EXPRESSION

KW - CAP-ANALYSIS

KW - TRANSCRIPTIONAL LANDSCAPE

KW - FUNCTIONAL ANNOTATION

KW - NATIONAL CENTER

KW - HUMAN GENOME

KW - RNA-SEQ

KW - DATABASE

KW - ONTOLOGIES

KW - MOUSE

U2 - 10.1186/s13059-014-0560-6

DO - 10.1186/s13059-014-0560-6

M3 - Article

SN - 1465-6906

VL - 16

JO - Genome Biology

JF - Genome Biology

M1 - 22

ER -

Gateways to the FANTOM5 promoter level mammalian expression atlas

Abstract / Description of output

Keywords / Materials (for Non-textual outputs)

Access to Document

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Biolayout Express3d: a community resource for the network visulisation and analysis of biological data and pathways

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