Update of the FANTOM web resource: Expansion to provide additional transcriptome atlases

Marina Lizio, Imad Abugessaisa, Shuhei Noguchi, Atsushi Kondo, Akira Hasegawa, Chung Chau Hon, Michiel De Hoon, Jessica Severin, Shinya Oki, Yoshihide Hayashizaki, Piero Carninci, Takeya Kasukawa, Hideya Kawaji

Research output: Contribution to journalArticlepeer-review

132 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)D752-D758
JournalNucleic acids research
Issue numberD1
Publication statusPublished - Jan 8 2019

All Science Journal Classification (ASJC) codes

  • Genetics


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