SSTAR (Semantic catalogue of Samples, Transcription initiation And Regulators) hosts a collection of pages representing the complete sets of FANTOM5 samples (primary cells, tissues, cell lines), CAGE peaks (TSS regions), transcription factors, and ontologies. It also stores analysis results such as expression and co-expression of peaks, enrichment scores, and DNA motifs recognized by transcription factors. SSTAR provides lists of samples profiled in FANTOM5 as individual sample pages. Using SSTAR, researchers can access sample details investigated in the FANTOM5 and the analysis results in a similar manner to Wikipedia with a customized visualization and data export.
- Q1. 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 part of mouse encyclopedia project in Japan (see its history). In 2014, FANTOM5 unravelled the biggest collection of promoters across a wide range of samples.
- Q2. How do I access the FANTOM5 data?
- Interactive databases (interactive viewer and data exporter) and all the data files are collected in at latest
- Q3. Is there a web portal to visualize FANTOM5 analysis results?
- Yes, it is available at results
- Q4. 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.
- Q5. If I want to select a set of samples belonging to a certain ontology type, what do I do?
- SSTAR provides lists of the sample ontology terms (cell type, tissue, and disease ontologies) with hyperlinks to individual ontology term pages. Within each of those pages, detailed information are shown, and samples associated to the term based on FF Sample Ontology classification are listed. The ontology term page also shows the parent-children relationships via graphical interface.
- Q6. Where do I find gene information associated to the FANTOM5 samples?
- Simple keyword search of genes in SSTAR helps to find a gene page showing its associated CAGE peaks and their activity levels across all the samples, as well as basic gene information as obtained from EntrezGene.
- Q8. Is there a place to look at the expression levels of FANTOM5 samples?
- Yes, we provide ZENBU genome browser and UCSC mirror site. In addition, with BioLayout Express 3D it is possible to look at co-expression events in a sample/gene network fashion.
- Q9. How do I download data, or part of it?
- There are several options for this. Access the ftp site and download from there (see Q2); use TET tool to extract portions of the data; use BioMart to extract annotation only.