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Features that regulate gene expression, Demo

We’re going to have a look for regulatory features in the region of a gene and investigate their activity in different cell types. We’ll start by searching for the gene KPNA2 and jumping to the location tab. Zoom out a little to see the gene plus some flanking regions.

The Regulatory Build is shown by default.

In this region we can see a number of regulatory features, including a red promoter with pink promoter flanks, cyan CTCF binding sites, yellow enhancers and lilac TF binding sites (don’t worry if you have zoomed out further or not as far and can see more/less). Refer to the legend at the bottom to see what the colours mean.

You can also click on the regulatory features to learn more. Click on the red promoter to get a pop-up.

Click on the stable ID, ENSR00000097453, to jump to the Regulation tab.

Black and grey lines indicate the positions of transcription factor binding motifs (TFBMs). Black lines are verified, which means there is evidence of the TF binding at this locus in at least one studied cell type, whereas grey ones have not been observed. Click on a TFBM then the matrix ID to see the matrix as a pop-up window.

Close the motif pop-up and scroll down the page. We can see that this promoter is active in one out of the 118 cell types currently in Ensembl.

We can explore more detailed data in Details by cell type – click on the button at the top.

At the moment the page is not displaying any data as we haven’t chosen any cell types. Click on Configure Cell/Tissue to add more to the view.

We can add cells by clicking on them. Find them using the search or the alphabet ribbon. Let’s add a cell type where the promoter is inactive, aorta, and one where it’s active astrocytes. Once you’ve selected the cells, they will appear in the menu on the right, where you can easily view the list by clicking on the + and deselect them.

To choose the experiments to see data on, click on the Experiments tab at the top of the menu. You can navigate this the same as the Cell/Tissue tab, except that you have to choose between Histone modifications, Open Chromatin and Transcription Factors. Let’s Select all in all categories.

When you’ve chosen your experiments and cells, you can click on the green Configure track display button.

Now we can see the active feature in astrocytes compared to the inactive feature in aorta.