An improved version of PrESSTo, called SlideBase is now available at http://slidebase.binf.ku.dk
SlideBase offers selection of cell or tissue specific genomic elements using sliders for the following datasets:

PrESSto: Promoter Enhancer Slider Selector Tool

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

Human Promoter Expression Atlas

Human Promoters Selector Tool

The FANTOM 5 consortium has mapped transcription start sites (TSSs) and their usage in 573 human primary cells and 152 human post-mortem tissues to produce a comprehensive overview of mammalian gene expression across the human body. This has been done using cap analysis of gene expression (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. The PrESSTo tool allows for the selection of promoters expressed in specific sets of tissues or cells based on slider thresholding, where the number of promoter adhering to a given combination of expression thresholds for cells or tissue are update in real time.

For more information about the FANTOM promoter atlas, see:

Human Transcribed Enhancer Atlas

Human Enhancers Selector Tool

Because active enhancer regions are transcribed, we identified a distinct bidirectional CAGE pattern which could predict enhancer regions based on CAGE data. Because enhancer transcription is a powerful proxy of cell-specific enhancer activity, we could define an atlas of ~40.000 active, in vivo bidirectionally transcribed enhancers across the human body using the FANTOM5 panel of tissue and primary cell samples. As above, PrESSTo allows for the selection of enhancers expressed in one of many cells or tissues based on sliders.

For more information about the FANTOM enhancer atlas, see:

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

  • tracks where one facet is over-represented (similar, but not identical to so-called tissue-specific transcription)
  • tracks of enhancers used in a certain facet (but not necessarily over-represented)
  • tracks for ubiquitously used enhancers