Gateways to the FANTOM5 Promoter Level Mammalian Expression Atlas
Lizio et al. Genome Biology (2015) 16:22 DOI 10.1186/s13059-014-0560-6 SOFTWARE Open Access Gateways to the FANTOM5 promoter level mammalian expression atlas Marina Lizio1,2, Jayson Harshbarger1,2, Hisashi Shimoji1,2, Jessica Severin1,2, Takeya Kasukawa2, Serkan Sahin1,2, Imad Abugessaisa2, Shiro Fukuda1, Fumi Hori1,2, Sachi Ishikawa-Kato1,2, Christopher J Mungall5, Erik Arner1,2, J Kenneth Baillie7, Nicolas Bertin1,2,19, Hidemasa Bono10, Michiel de Hoon1,2, Alexander D Diehl13, Emmanuel Dimont12, Tom C Freeman7, Kaori Fujieda10, Winston Hide12,17, Rajaram Kaliyaperumal8, Toshiaki Katayama15, Timo Lassmann1,2,18, Terrence F Meehan6, Koro Nishikata16, Hiromasa Ono10, Michael Rehli9, Albin Sandelin11, Erik A Schultes8,14, Peter AC ‘t Hoen8, Zuotian Tatum8, Mark Thompson8, Tetsuro Toyoda16, Derek W Wright7, Carsten O Daub1, Masayoshi Itoh1,2,3, Piero Carninci1,2, Yoshihide Hayashizaki1,3, Alistair RR Forrest1,2*, Hideya Kawaji1,2,3,4* and the FANTOM consortium 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. Introduction ontologies [10]). However, the ability of these surveys to One of the most comprehensive ways to study the mo- quantify RNA abundance was limited mainly due to se- lecular basis of cellular function is to quantify the pres- quencing performance.
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