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Regulation

Example page

Gene regulation information from the following sources are shown in this view:

  • Ensembl Regulatory Build - derived from data from projects such as ENCODE and Roadmap Epigneomics
  • VISTA- a set of experimentally determined enhancers for human and mouse
  • Tarbase - miRNA targets for human and mouse
  • Fantom TSS/Enhancers for human.
  • REDfly - cis-regulatory modules and transcript factor binding sites for Drosophila
  • GTEX - eQTLs.

The graphical display shows sequences from the sources listed above that are potentially involved in gene regulation. Click on any block for information about that sequence. Ensembl transcripts are shown at the top of the view. Configure this page allows track selection.

For human this includes Regulatory Features from the Ensembl Regulatory Build (Zerbino et al. 2015). These sequences are assigned a stable ID beginning with ENSR, and reflect information from various cell types. The Reg. Feats track combines evidence from all cell types into predicted regulatory elements, while the regulatory features for individual cell types are shown in individual tracks in the diagram (e.g. GM06990, etc.) Regulatory features are also shown in the table below.

Click on any block in the 'Reg. Feats' track or any ENSR ID to jump to more detailed information about the regulatory feature.

In human, eQTLs from GTEX are displayed. You can add different tissues by clicking on Configure this page. eQTL variants are shown as a Manhattan plot of the p-value, against a log scale with lower (ie more significant) p-values higher up. Click on the variants to see the p-value and to click through for more information about the variant.

Data sets can also be displayed in a genomic context by using the Region in detail view, or mined from the Ensembl Regulation (funcgen) database using our API. BioMart allows export of these features (start with the functional genomics database). Find an introduction to BioMart on our tutorials page.