- What is FANTOM?
- FANTOM (Functional ANnoTation Of the Mammalian genome) is a worldwide collaborative project aiming at identifying all functional elements in mammalian genomes. It started at RIKEN Yokohama, as a part of mouse encyclopedia project in Japan (see its history). In 2014, FANTOM5 unraveled the biggest collection of promoters across a wide range of samples.
- How do I access the FANTOM5 data?
- Interactive databases (interactive viewer and data exporter) and all the data files are collected in at https://fantom.gsc.riken.jp/5/
- How do I search for sample details?
- The best way is to use SSTAR. Individual sample pages store basic details such as donor age, sex, and RNA quality metrics as well as analysis results about transcription regulation. Supplementary table 1 of the promoterome paper at Nature lists all the samples profiled in FANTOM5 phase 1 and some key attributes. This is also a good starting point.
- Is there a place to look at the expression levels of transcripts/genes/whatever in the FANTOM5 samples?
- Yes, the ZENBU genome browser allows you to look at expression originating from any genomic region across the sample collection. SSTAR and the TET tool also allow you to extract expression profiles of individual promoters (SSTAR promoter page) or the entire set (TET tool). In addition, with BioLayout Express 3D it is possible to look at co-expression events in a sample/gene network fashion.
- How do I download data, or part of it?
- There are several options for this. Access the ftp site and download from there (see https://fantom.gsc.riken.jp/5/data/); use TET tool to extract portions of the data; use BioMart to extract annotation only.
- How do I cite usage of FANTOM5 data or resources?
- In addition to relevant papers, please cite the following papers for using data obtained from this site:
[Latest version] Lizio M, et al. Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. Nucleic Acids Res. 47: D752–D758 (2019). 10.1093/nar/gky1099
[Initial version] Lizio M, et al. Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol 16: 22 (2015). 10.1186/s13059-014-0560-6
- I am able to provide a cell type that isn't covered in the collection. Can I still participate?
- Technically phase 1 is finished, but there may be opportunities to add new rare cell samples in the future. Please contact us at email@example.com.
- What is the difference between p1@MYB, p2@MYB and why do some cluster just have p@chrXXXXX instead?
- FANTOM5 peaks that are near the 5' ends of known gene/transcript models are annotated with the gene name, those that are not are anonymous. The p1, p2, p3 terminology corresponds to the promoters for the same gene ranked by their level of tag evidence. p1@MYB has more support than p2@MYB etc.
- I have another question. I think I have found an error or bug. Who should I contact?
- Please contact firstname.lastname@example.org. Please include the URL and short description of the problem.