243 ENCODE ChIP-Seq Experiments

The ENCODE project is generating an immense amount of data.  ChIP-Seq, ChIP-ChIP, and RNA-Seq experiments are yielding an exciting number of sequences that may be involved in gene regulation.  Trying to look at these data individually would be a lot of work, and less powerful, than viewing these data in combination.  The Ensembl Regulatory Build takes data such as CTCF binding sites, DNaseI hypersensitive sites, transcription factor binding sites, and histone modification profiles, and integrates these data into ‘regulatory features’.  The result is for any given regulatory feature in a specific region of the human genome, our users can learn 1) if there is data supporting that sequence as being involved in gene regulation (for example,  is it promoter associated) and  2) how much data supports the sequence as a regulatory feature.

For example, if we zoom in to BRCA2 in the Ensembl region in detail view, the regulatory feature at the 5’ end of the BRCA2-003 transcript is supported by data from numerous experiments (shown in the figure below).  Click on the grey block in the Reg. Feats. track in the region in detail view to see them.






You can even view regulatory features for a specific cell type.  Click on the Configure this page tool button at the left of the region in detail view to do so.  Or, try the regulation tab (get there by clicking on a regulatory feature’s stable ID, such as ENSR00000054736 in the image above).

Questions or comments about these data or views are welcome.  Reply to this post, or email our helpdesk by using the Contact us link at the top right of this blog.

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