FANTOM5 SSTAR is now unavailable. We apologize for your inconvenience.

The current FANTOM web portal tentatively look different from the previous one, but the databases, the data sets, and the data viewers are  available as before . Please don’t hesitate to use them in the same way. Hyperlinks to individual projects (FANTOM1-5) is here:

FANTOM5          FANTOM4          FANTOM3          FANTOM2          FANTOM1

What happened? - One of our servers that provides this FANTOM portal site had a trouble, and we are in its recovery stage. We didn’t find any problems in the other systems, except for the portal site. Please contact us <fantom-help@riken.jp> for any questions.

FANTOM5

We are complex multicellular organisms composed of ~400 distinct cell types. This diversity of cell types allow us to see, think, hear, fight infections etc. yet all of this is encoded in the same genome. The difference between all these cells is what parts of the genome they use – for instance, neurons use different genes than muscle cells, and therefore they work very differently. In FANTOM5, we have systematically investigated exactly what are the sets of genes used in virtually all cell types across the human body, and the genomic regions which determine where the genes are read from. We aim to use this information to build transcriptional regulatory models for every primary cell type that makes up a human.

FANTOM5 collection

A collection of FANTOM5 articles published in the Nature Publishing Group (NPG) is provided.

shortcut links

organism

atlas

tools

data files

human

Promoter atlas

( SSTAR , sample list )

Enhancer atlas

( SlideBase )

lncRNA atlas

( CAT )

miRNA atlas

Cell Connectome

Zenbu  

( Time course )

TET

BioLayout

BioMart

UCSC Genome Browser

( GRCh37, GRCh38 , with ChIP-Atlas)

Raw data

( GRCh37 , GRCh38 )

Promoter (CAGE peaks)

(GRCh37  , GRCh38 )

Enhancer

( GRCh37  , GRCh38 )

mouse

Promoter atlas

( SSTAR , sample list )

miRNA atlas

Zenbu  

( Time course )

TET

BioMart

UCSC Genome Browser

( mm9  , mm10 )

Raw data

( GRCm37  , GRCm38  )

Promoter (CAGE peaks)

( GRCm37  , GRCm38 )

Enhancer

( GRCm37  , GRCm38 )

rat

Promoter atlas

( SSTAR , sample list )

Zenbu

TET

UCSC Genome Browser

Raw data

Promoter (CAGE peaks)

dog

Promoter atlas

( SSTAR , sample list )

TET

UCSC Genome Browser

Raw data

Promoter (CAGE peaks)

chicken

Promoter atlas

( SSTAR , sample list )

Zenbu

Raw data

Promoter (CAGE peaks)

rhesus monkey

Promoter atlas

( SSTAR, sample list )

UCSC Genome Browser

Raw data

Promoter (CAGE peaks)

Views and Data

Various resources are now available to access FANTOM5 data

Zenbu

A new data integration, data processing, and expression enhanced visualization system with secured data upload and sharing designed for big data genomics projects (FANTOM5, FANTOM4, FANTOM3, ENCODE). Primary data visualization system for FANTOM5. Direct links for FANTOM5 promoterome views: hg19  and mm9 . Direct links for FANTOM5 timecourse views: hg19  and mm9

SSTAR

(Semantic catalogue of Samples, Transcription initiation, And Regulations) An interface to explore the cell type, co-expression cluster specific annotations, motifs and transcription factors. Summary of FANTOM5 time course samples.

FANTOM CAT Browser

An web application allows users to browse genes, view their genomic loci through ZENBU, filter by their annotations, intersect them with their associated sample ontologies or traits, and download the relevant data.

FANTOM5 miRNA atlas

The FANTOM5 integrated miRNA expression atlas shows the expression patterns of miRNAs profiled by sequencing short RNA libraries obtained from human and mouse samples. Both the sRNA expression profile of the mature miRNA and the CAGE expression profile of its associated promoter can be visualized. Enriched and depleted cell ontology categories are shown for each miRNA to summarize the expression profile.

Cell Connectome Visualization

We constructed a signalling map between 144 major primary cell types in human connected through interacting pairs of secreted ligands and cell-surface receptors. Our visualization tool shows what ligands/receptors are present in given cells and what cells are connected to each other by the interacting pairs. Data is also available for downloading.

Files

Selected datafiles for FANTOM5. Alternatively you may view the data file server directly at /5/datafiles/

Other Resources

TrackHub

FANTOM5 promoters, enhancers, lncRNAs and FANTOM5 cell lines  on the UCSC Genome Browser  Database, Asia mirror

TET

A system for extracting subsets of data from selected FANTOM5 data files including phase 1 and phase 2 expression tables.

Transcribed Enhancer Atlas

A database describing enhancer regions with samples over the whole human body.

Additional relevant links

BioMart , RIKEN MetaDatabase , nanopublication , and FANTOM5 BioLayout .

How to cite

In addition to relevant papers , please cite the following paper for using data obtained from this site:

Lizio M, et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol 16: 22 (2015). 10.1186/s13059-014-0560-6

Lizio M, et al. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Res 45: D737-D743 (2017). 10.1093/nar/gkw995

Contact us: fantom-help@riken.jp