Introduction to 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 Phase 2
Using a comprehensive analysis of RNA expression in different cell types, scientist from the RIKEN-led FANTOM5 consortium have made major strides toward resolving an outstanding mystery in biology. In the work, published in Science, they showed that when cells undergo phenotype changes such as differentiation into specialized cell types, the initial activation happens at DNA regions called enhancers, a type of regulatory “switches” which are typically located far from the genes that they activate.
FANTOM5 Phase 1
Using Cap Analysis of Gene Expression (CAGE) we have mapped the sets of transcripts, transcription factors, promoters and enhancers active in the majority of mammalian primary cell types and a series of cancer cell lines, and tissues, which is described in two landmark papers in Nature. Around 30 publications from the project cover areas as diverse as primary cells, gene families, genome wide observations on promoter features and new bioinformatics tools.
A collection of FANTOM5 articles published in the Nature Publishing Group (NPG) is provided.
A system for extracting subsets of data from selected FANTOM5 data files including phase 1 and phase 2 expression tables.
A BioMart instance to download user defined subsets of the FANTOM5 promoters.
A database describing enhancer regions with samples over the whole human body.
How to citeIn 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: expansion to provide additional transcriptome atlases. Nucleic Acids Res 47: D752–D758 (2019). 10.1093/nar/gky1099