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Protein Function Prediction

Volume 1611 of the series Methods in Molecular Biology pp 199-217

Date:

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

  • Imad AbugessaisaAffiliated withDivision of Genomic Technologies, RIKEN Center for Life Science Technologies
  • , Shuhei NoguchiAffiliated withDivision of Genomic Technologies, RIKEN Center for Life Science Technologies
  • , Piero CarninciAffiliated withDivision of Genomic Technologies, RIKEN Center for Life Science Technologies Email author 
  • , Takeya KasukawaAffiliated withDivision of Genomic Technologies, RIKEN Center for Life Science Technologies Email author 

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Abstract

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.

Keywords

FANTOM5 Genomics Transcriptome Genome annotation CAGE TSS Promoter Enhancer