Gateways to the FANTOM5 promoter level mammalian expression atlas

被引：569

作者：

Lizio, Marina ^{[1
,2
]}

Harshbarger, Jayson ^{[1
,2
]}

Shimoji, Hisashi ^{[1
,2
]}

Severin, Jessica ^{[1
,2
]}

Kasukawa, Takeya ^{[2
]}

Sahin, Serkan ^{[1
,2
]}

Abugessaisa, Imad ^{[2
]}

Fukuda, Shiro ^{[1
]}

Hori, Fumi ^{[1
,2
]}

Ishikawa-Kato, Sachi ^{[1
,2
]}

Mungall, Christopher J. ^{[5
]}

Arner, Erik ^{[1
,2
]}

Baillie, J. Kenneth ^{[7
,8
]}

Bertin, Nicolas ^{[1
,2
,21
]}

Bono, Hidemasa ^{[11
]}

de Hoon, Michiel ^{[1
,2
]}

Diehl, Alexander D. ^{[15
]}

Dimont, Emmanuel ^{[14
]}

Freeman, Tom C. ^{[7
,8
]}

Fujieda, Kaori ^{[11
]}

Hide, Winston ^{[14
,19
]}

Kaliyaperumal, Rajaram ^{[9
]}

Katayama, Toshiaki ^{[17
]}

Lassmann, Timo ^{[1
,2
,20
]}

Meehan, Terrence F. ^{[6
]}

Nishikata, Koro ^{[18
]}

Ono, Hiromasa ^{[11
]}

Rehli, Michael ^{[10
]}

Sandelin, Albin ^{[12
,13
]}

Schultes, Erik A. ^{[9
,16
]}

Hoen, Peter A. C't ^{[9
]}

Tatum, Zuotian ^{[9
]}

Thompson, Mark ^{[9
]}

Toyoda, Tetsuro

Wright, Derek W. ^{[7
,8
]}

Daub, Carsten O. ^{[1
]}

Itoh, Masayoshi ^{[1
,2
,3
]}

Carninci, Piero ^{[1
,2
]}

Hayashizaki, Yoshihide ^{[1
,3
]}

Forrest, Alistair R. R. ^{[1
,2
]}

Kawaji, Hideya ^{[1
,2
,3
,4
]}

机构：

[1] RIKEN, Om Sci Ctr, Yokohama Inst, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan

[2] RIKEN, Ctr Life Sci Technol, DGT, Yokohama, Kanagawa 2300045, Japan

[3] RIKEN, Prevent Med & Diag Innovat Program, Wako, Saitama 3510198, Japan

[4] RIKEN, Adv Ctr Comp & Commun, Prevent Med & Appl Genom Unit, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan

[5] Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA

[6] European Bioinformat Inst, Mouse Informat European Mol Biol Lab, Cambridge CB10 1SD, England

[7] Univ Edinburgh, Roslin Inst, Edinburgh EH25 9RG, Midlothian, Scotland

[8] Univ Edinburgh, Royal Dick Sch Vet Studies, Edinburgh EH25 9RG, Midlothian, Scotland

[9] Leiden Univ, Med Ctr, Dept Human Genet, BioSemant Grp, NL-2333 ZA Leiden, Netherlands

[10] Univ Hosp Regensburg, Dept Internal Med 3, D-93042 Regensburg, Germany

[11] Res Org Informat & Syst, Database Ctr Life Sci, Mishima, Shizuoka 4118540, Japan

[12] Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark

[13] Univ Copenhagen, Biotech Res & Innovat Ctr, Sect Computat & RNA Biol, DK-2200 Copenhagen, Denmark

[14] Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA

[15] SUNY Buffalo, Sch Med & Biomed Sci, Dept Neurol, Buffalo, NY 14203 USA

[16] Leiden Univ, Leiden Inst Adv Comp Sci, BioSemant Grp, NL-2333 CA Leiden, Netherlands

[17] Res Org Informat & Syst, Database Ctr Life Sci, Kashiwa, Chiba 2770081, Japan

[18] RIKEN, Adv Ctr Comp & Commun, Integrated Database Unit, Wako, Saitama 3510198, Japan

[19] Univ Sheffield, Sheffield Inst Translat Neurosci, Sheffield S10 2HQ, S Yorkshire, England

[20] Univ Western Australia, Telethon Kids Inst, Perth, WA 6008, Australia

[21] Natl Univ Singapore, Canc Sci Inst Singapore, Singapore 117599, Singapore

来源：

GENOME BIOLOGY | 2015年 / 16卷

基金：

英国惠康基金; 英国生物技术与生命科学研究理事会;

关键词：

ANALYSIS GENE-EXPRESSION; CAP-ANALYSIS; TRANSCRIPTIONAL LANDSCAPE; FUNCTIONAL ANNOTATION; RNA-SEQ; ONTOLOGIES; DATABASE; MOUSE; VISUALIZATION; CONSTRUCTION;

D O I：

10.1186/s13059-014-0560-6

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：14

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