PrESSto: Promoter Enhancer Slider Selector Tool

Select enhancers and promoters based on tissue and cell specificity using sliders.

About PrESSTo

The FANTOM5 set

The FANTOM5 project aimed to make a TSS-level transcription atlas using in-vivo samples primary cells, tissues and cell lines over the whole human body, using Heliscope single molecule sequencing . A more thorough description is given by The FANTOM 5 Consortium and the RIKEN PMI and CLST (DGT) publication. The CAGE TSS collection is available at http://fantom.gsc.riken.jp/5/

Cite us

If you use this resource, please cite:


Human Promoter Expression Atlas

A database describing promoter regions defined by CAGE tags in the FANTOM5 project, with samples over the whole human body

Concept and background

The FANTOM5 consortium have extracted RNA transcripts from a multitude of different primary cells and tissues using the CAGE experiment (short for Cap Analysis of Gene Expression). As a result, mappings of transcription start sites and their usage in human primary cells and post-mortem tissues were produced in order to construct a comprehensive overview of gene expression across the human body. This has been done using CAGE and single-molecule sequencing. The result is a unique gene expression profile atlas, focused specifically on core promoter utilization. CAGE has advantages over RNA-seq or microarrays for this purpose, because it permits separate analysis of multiple promoters linked to the same gene. In consequence, for each promoter we have a measure of expression within each primary cell and tissue and based on the expression levels a promoter can be specific to a set of primary cells and tissues or can be broadly expressed. Expression levels are measured in CAGE tags (simple or normalized). The expression levels used in PrESSTo are measured in TPM (tags per million). In addition, the mapping and annotation process has found promoters associated with known genes as well as anonymous (or novel) promoters, which are not close to known genes. In PrESSTo we have simplified the samples by aggregating anatomically/functionally similar cells and tissues into “facets”. Examples of cell facets are: neurons, T cells or monocytes; example of tissue facets are: brain, liver or heart tissue.

Resources

Human Promoters Selector: Using sliders, it is possible to define promoter sets with custom expression constraints. For instance, moving the liver slider to 10% and the intestine slider to 50% results in all promoters where at least 10% of CAGE tags are from liver at at least 50% are from intestine. The resulting promoter set can be further filtered by genomic location. The promoters can be downloaded as BED and sequence files, viewed in the UCSC and ZENBU browsers. In addition, basic motif discovery using MEME can be performed on the resulting promoter set. For each individual promoter, potential overlaps with enhancers and SNPs are shown. A promoter can be associated with a known gene or be classified as a novel promoter.


Human Transcribed Enhancer Atlas

A database describing enhancer regions defined by CAGE tags in the FANTOM5 project, with samples over the whole human body

Concept and background

Because active enhancer regions are transcribed, we identified a distinct bidirectional CAGE pattern which could predict enhancer regions based on CAGE data not associated with promoters. Because enhancer transcription is a powerful proxy of cell-specific enhancer activity, we could define an atlas of active, in vivo bidirectionally transcribed enhancers across the human body (see Andersson et al) using the FANTOM5 panel of tissue and primary cell samples. Similar to promoters, for each enhancer we have a measure of expression within each primary cell and tissue and based on the expression levels, an enhancer can be specific to a set of primary cells and tissues or can be broadly (or ubiquitously) expressed. Expression levels are measured in CAGE tags (simple or normalized). The expression levels used in PrESSTo are measured in TPM (tags per million). In PrESSTo we have simplified the samples by aggregating anatomically/functionally similar cells and tissues into “facets”. Examples of cell facets are: neurons, T cells or monocytes; example of tissue facets are: brain, liver or heart tissue. The transcribed enhancer atlas holds ~40.000 transcribed enhancers across the human body. This is a joint project between the Sandelin group at the Bioinformatics Centre, University of Copenhagen, the Rehli group at Universitätsklinikum Regensburg, the FANTOM5 consortium and the RIKEN OMICS Science Centre, RIKEN Yokohama institute

Using bidirectional transcription to find enhancers

Simplified, enhancers are detected by locating CAGE clusters that are up to two nucleosome-deficient regions apart, with balanced transcription on both strands. These two boundaries correspond remarkably well with nucleosome borders.

Resources

Human Enhancers Selector: Using sliders, it is possible to define enhancer sets with custom expression constraints. For instance, moving the liver slider to 10% and the intestine slider to 50% results in all enhancers where at least 10% of CAGE tags are from liver at at least 50% are from intestine. The resulting enhancer set can be further filtered by genomic location. The enhancers can be downloaded as BED and sequence files, viewed in the UCSC and ZENBU browsers. In addition, basic motif discovery using MEME can be performed on the resulting enhancer set. For each individual enhancer, potential overlaps with promoters and SNPs are shown.

Pre-defined enhancer sets and TSS-enhancer association tracks: Using statistical methods, we have defined several tracks used in Andersson et al. These include: