The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers

  • Imad Abugessaisa
  • Shuhei Noguchi
  • Piero CarninciEmail author
  • Takeya KasukawaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1611)


The Functional Annotation of the Mammalian Genome 5 (FANTOM5) project conducted transcriptome analysis of various mammalian cell types and provided a comprehensive resource to understand transcriptome and transcriptional regulation in individual cellular states encoded in the genome.

FANTOM5 used cap analysis of gene expression (CAGE) with single-molecule sequencing to map transcription start sites (TSS) and measured their expression in a diverse range of samples. The main results from FANTOM5 were published as a promoter-level mammalian expression atlas and an atlas of active enhancers across human cell types. The FANTOM5 dataset is composed of raw experimental data and the results of bioinformatics analyses. In this chapter, we give a detailed description of the content of the FANTOM5 dataset and elaborate on different computing applications developed to publish the data and enable reproducibility and discovery of new findings. We present use cases in which the FANTOM5 dataset has been reused, leading to new findings.


FANTOM5 Genomics Transcriptome Genome annotation CAGE TSS Promoter Enhancer 



FANTOM5 was made possible by a Research Grant for RIKEN Omics Science Center from MEXT to Yoshihide Hayashizaki and a Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT, Japan to Yoshihide Hayashizaki and to the RIKEN Center for Life Science Technologies. This study is also supported by Research Grants from the Japanese Ministry of Education, Culture, Sports, Science and Technology through RIKEN Centre for Life Science Technologies, Division of Genomic Technologies. We would like to thank all the members of the FANTOM5 consortium for contributing to the generation of samples and analysis of the data-set and thank GeNAS for data production.


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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Division of Genomic TechnologiesRIKEN Center for Life Science TechnologiesYokohamaJapan

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