Description - FANTOM5

Regulated transcription controls the diversity, developmental pathways, and spatial organisation of the hundreds of cell types that make up a mammal. In FANTOM5 ( http://fantom.gsc.riken.jp/5/ ), we mapped transcription start sites (TSS) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of gene expression across the human body by using single molecule sequencing. This datahub is set up to provide the TSS activities in individual biological states and the identified regions. Please visit the web site for further data exploration and with details.

Methods

5'-end of the mapped CAGE reads are counted at a single base pair resolution (CTSS, CAGE tag starting sites) on the genomic coordinates, which represent TSS avtivities in the sample. Identified peaks in the whole set of TSS (or CAGE) profiles are classified into two categories - robust and permissive - based on evidence of read counts. The robust set is used for expression analysis, ant the permissive set is used for TSS exploration.

The structure of tracks as below:

Summary tracks
- Total counts and TPM (tags per million) in all the samples
- Maximum counts and TPM among the samples
- CAGE peaks, the permissive set
Individual profiles (CAGE read counts and TPM)
- Cell Line hCAGE
- Cell Line LQhCAGE
- fractionation hCAGE
- Primary cell hCAGE
- Primary cell LQhCAGE
- Time course hCAGE
- Tissue hCAGE

Data files

Credits

Please send us any questions regarding to this trackHub and underlying data.

References

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, et al. Science. 2015 Feb 27;347(6225): 1010-4. doi: 10.1126/science.1259418. Epub 2015 [PMID: 25678556]

Gateways to the FANTOM5 promoter level mammalian expression atlas. Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, et al. Genome Biol. 2015 Jan 5;16:22. doi: 10.1186/s13059-014-0560-6. [PMID: 25723102]

Forrest ARR, Kawaji H, Rehli M, Baillie JK, de Hoon MJL, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M et al. A promoter level mammalian expression atlas, Nature http://dx.doi.org/ 10.1038/nature13182.