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. 2019 Jan 8;47(D1):D752-D758.
doi: 10.1093/nar/gky1099.

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

Marina Lizio  1 , Imad Abugessaisa  1 , Shuhei Noguchi  1 , Atsushi Kondo  1 , Akira Hasegawa  1 , Chung Chau Hon  1 , Michiel de Hoon  1 , Jessica Severin  1 , Shinya Oki  2 , Yoshihide Hayashizaki  3 , Piero Carninci  1 , Takeya Kasukawa  1 , Hideya Kawaji  1   3
Affiliations

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

Marina Lizio et al. Nucleic Acids Res. .

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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Figures

Figure 1.
Figure 1.
Schematic view of the FANTOM5 atlases and data. The atlases are indicated by book icons, and the data sets are indicated by gray boxes. New data sets and atlases are indicated in the top panel.
Figure 2.
Figure 2.
Using the FANTOM CAT browser to explore lncRNAs associated with classical monocytes. (A) Browse the ontology list page by clicking on ‘Ontologies’ on the landing page; (B) filter for ‘classical monocytes’; (C) list of genes associated with ontology CL:0000860 classical monocytes; (D) filter for gene classes of ‘lncRNA’; (E) sort genes by their level of association with classical monocytes; (F) summary page of the lncRNA gene CATG00000102578.1, with highest level of association to classical monocytes (http://fantom.gsc.riken.jp/cat/v1/#/genes/CATG00000102578.1); (G) annotation summary of CATG00000102578.1; (H) expression level of CATG00000102578.1 in FANTOM5 samples, with samples of classical monocytes highlighted; (I) dynamic expression pattern of CATG00000102578.1 in FANTOM5 samples.
Figure 3.
Figure 3.
The FANTOM5 miRNA expression atlas. The annotated miRNA promoter, expression profile and results of the cell-type enrichment analysis are shown by using miRNA hsa-miR-9-5p as an example (http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human).
Figure 4.
Figure 4.
MCF-7 cells: integrated view of transcriptome and epigenetic marks. The data were obtained from ChIP-Atlas, which covers all ChIP-seq experiments deposited in SRA, in addition to FANTOM5. The view of EGR-1 locus is displayed by the UCSC Genome Browser via the trackHub framework(https://genome-asia.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://fantom.gsc.riken.jp/5prim/external/CellLines-CAGE-with-epigenome/hub.txt).
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