TY - JOUR
T1 - Update of the FANTOM web resource
T2 - Expansion to provide additional transcriptome atlases
AU - Lizio, Marina
AU - Abugessaisa, Imad
AU - Noguchi, Shuhei
AU - Kondo, Atsushi
AU - Hasegawa, Akira
AU - Hon, Chung Chau
AU - De Hoon, Michiel
AU - Severin, Jessica
AU - Oki, Shinya
AU - Hayashizaki, Yoshihide
AU - Carninci, Piero
AU - Kasukawa, Takeya
AU - Kawaji, Hideya
N1 - Funding Information:
Research grants to RIKEN Center for Life Science Technologies, RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Integrative Medical Sciences from the Japan Ministry of Education, Culture, Sports, Science and Technology (MEXT); Japan Society for the Promotion of Science KAKENHI Grants [16H02902, 16K12529 to H.K.]; Research grant from National Bioscience Database Center of the Japan Science and Technology Agency. Funding for open access charge: MEXT.
Publisher Copyright:
© 2018 The Author(s).
PY - 2019/1/8
Y1 - 2019/1/8
N2 - The FANTOM web resource (http://fantom.gsc.riken.jp/) was developed to provide easy access to the data produced by the FANTOM project. It contains the most complete and comprehensive sets of actively transcribed enhancers and promoters in the human and mouse genomes. We determined the transcription activities of these regulatory elements by CAGE (Cap Analysis of Gene Expression) for both steady and dynamic cellular states in all major and some rare cell types, consecutive stages of differentiation and responses to stimuli. We have expanded the resource by employing different assays, such as RNA-seq, short RNA-seq and a paired-end protocol for CAGE (CAGEscan), to provide new angles to study the transcriptome. That yielded additional atlases of long noncoding RNAs, miRNAs and their promoters. We have also expanded the CAGE analysis to cover rat, dog, chicken, and macaque species for a limited number of cell types. The CAGE data obtained from human and mouse were reprocessed to make them available on the latest genome assemblies. Here, we report the recent updates of both data and interfaces in the FANTOM web resource.
AB - The FANTOM web resource (http://fantom.gsc.riken.jp/) was developed to provide easy access to the data produced by the FANTOM project. It contains the most complete and comprehensive sets of actively transcribed enhancers and promoters in the human and mouse genomes. We determined the transcription activities of these regulatory elements by CAGE (Cap Analysis of Gene Expression) for both steady and dynamic cellular states in all major and some rare cell types, consecutive stages of differentiation and responses to stimuli. We have expanded the resource by employing different assays, such as RNA-seq, short RNA-seq and a paired-end protocol for CAGE (CAGEscan), to provide new angles to study the transcriptome. That yielded additional atlases of long noncoding RNAs, miRNAs and their promoters. We have also expanded the CAGE analysis to cover rat, dog, chicken, and macaque species for a limited number of cell types. The CAGE data obtained from human and mouse were reprocessed to make them available on the latest genome assemblies. Here, we report the recent updates of both data and interfaces in the FANTOM web resource.
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U2 - 10.1093/nar/gky1099
DO - 10.1093/nar/gky1099
M3 - Article
C2 - 30407557
AN - SCOPUS:85059798120
SN - 0305-1048
VL - 47
SP - D752-D758
JO - Nucleic acids research
JF - Nucleic acids research
IS - D1
ER -