How can I view and download regulation data?
Genomic features related to gene regulation, such as promoters and enhancers, and their activity across different cell types (epigenomes) can be found in Ensembl.
Processed primary data supporting the Regulatory build, such as peaks and signals from ChIP-seq, DNase-seq, and ATAC-seq experiments are also available.
There are different ways to access to regulation data:
The browser (for release 116 and before):
Regulation tracks for release 116 are available in Region in detail and other views such as in the gene tab.
For each feature, you can access detailed information and activity annotation by clicking the feature ID in the pop-up menu of the feature of interest.
To add tracks to the browser, you can click the Configure this page link in the left-hand side menu. Scroll down to the Regulation section to see the data available for a given species. The Regulatory Features track is enabled by default. Primary data and activity tracks for different cell types (epigenomes) can be enabled/disabled by selecting them in the Activity by Cell/Tissue panel. The data can be shown as signal profiles and peak calls.
For some species it is also possible to explore motif features predicted by combining position weight matrices (PWMs) and ChIP-seq data. The motifs track can be enabled/disabled when configuring the page. Motif features are displayed as black segments in the motif features track. Clicking on a particular motif feature will highlight the corresponding PWM in the pop-up menu.
The Regulation subsite
Regulation tracks are also available in the Ensembl Regulation subsite.
For each available species, you can explore annotated features and their predicted activity in different cell types (epigenomes). The subsite also offers detailed metadata linked to the analysed cell types (epigenomes) and to the experiment datasets and biosamples of the primary data that was processed, with links to the source repositories.
Other access for release 116
Primary data files (peaks and signals), regulatory features annotation and cell-type (epigenome) activity can be downloaded from the Ensembl FTP site.
BioMart provides another option for regulation data retrieval.
If you have any other questions about Ensembl, please do not hesitate to contact our HelpDesk. You may also like to subscribe to the developers' mailing list.