Accessing Ensembl Regulatory Annotation

Regulation data in Ensembl can be accessed through:

• The Ensembl Browser (see below)
• BioMart (Ensembl Regulation database).
• Perl APIs, including the Regulation API.

Browser access

Location Tab

You can configure the Region in detail panel to display tracks linked to regulation. The Regulation tracks are grouped into subdivisions:

• Regulatory Features: these can be visualised using the 'Regulatory Build' track.
• Activity Levels: select the cell type/line of interest and display the activity levels for each regulatory feature defined in the Regulatory Build.
• Segmentation Features: select the cell type/line of interest and display the genomic state assignment in the region.
• Open Chromatin and Transcription Factor Binding Sites (TFBS): display of signal or peaks from assays measuring open chromatin (DNAse-seq) or transcription factor binding (ChIP-seq) in various cell types/lines.
• Histones and Polymerases: display of signal or peaks from experimental ChIP-seq assays measuring histone marks/modifications or binding of RNA Polymerases II and III.
• DNA Methylation: RRBS and WGBS methylation tracks.
• Other regulatory regions: imported tracks from external databases.

Gene tab

Click on the Regulation link in the left hand side menu to view the regulatory features and eQTLs in the vicinity of your gene.

Regulation tab

Clicking on a regulatory feature will open a Regulation tab with information about the evidence supporting that regulatory feature as well as cell-specific activity estimates. Different views can be selected:

• Summary: this view displays the selected regulatory feature and a summary of its regulatory activity across cell types.
• Details by cell type: this view displays activity tracks for the regulatory feature in selected cell types. You can display more cell types by clicking on the Configure this page button above the image.
• Feature Context: this view displays regulatory features in a wider context around the chosen regulatory feature.
• Source Data: this view displays the list of source data for the chosen regulatory feature.