Update of the FANTOM Web Resource: Expansion to Provide Additional Transcriptome Atlases

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2018 Nov 9

PMID 30407557

Citations 126

Authors

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

Affiliations

Soon will be listed here.

Abstract

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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