How can I view and download gene regulation data... and where did it come from?
Sequences potentially involved in gene regulation such as promoters and enhancers can be found in Ensembl. These are based on experiments from the ENCODE project. The Ensembl Regulatory Build integrates data from various sources (e.g. ENCODE, Roadmap Epigenomics etc.), over different cell types for both human and mouse. You can also find the original data supporting the Regulatory Build.
Where available, there are additional features for human, mouse, and fly (e.g. cisRED, miRNA targets, VISTA enhancers, and REDfly).
Regulation tracks are available in Region in detail and other views such as the Regulation view in the gene tab. Turn tracks on by clicking 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.
Human and mouse
The Ensembl Regulatory Feature tracks display candidate regions likely to be involved with gene regulation such as potential promoters, enhancers, and insulators. These are the output of the Ensembl Regulatory Build The original data supporting the regulatory build are grouped under Open chromatin & Transcription factor binding sites or Histones & Polymerases. The data can be shown as signal profiles or peak calls.
Once these data tracks are drawn, peak summits are indicated by a pair of small triangle pointers when available. Position weight matrices (PWMs) for TFBS peaks and Regulatory Features are mapped as part of the Regulatory Build and displayed as vertical black bars. Clicking on a vertical black bar will highlight the corresponding PWM in the pop up menu.
Ensembl also hosts the complementary genome segmentation state analysis, which provides a single track summary of the functional architecture of the human genome.
Data are accessible using the Perl API.
Alternatively, download these data from the Ensembl ftp site.
BioMart provides another tool for regulation data retrieval.