Part D: Work with region tracks

In this part of the tutorial, you will load two BED files associated with the E. coli assembly.

• MG1655_m56_v3.prophage-regions.bed. contains ten regions or intervals corresponding to the locations of prophages within the genome of this particular strain of E. coli.

• MG1655_m56_v3.Sigma32_regulon.bed contains regions corresponding to genes that are known to be induced by heat shock (i.e., high temperatures).

Each BED file will appear as a separate Region track in GenVision Pro, just like the Features and Coverage tracks discussed in earlier parts of this tutorial.

1. BED files must be added one at a time. Select File > Add Track. Navigate to and double-click on MG1655_m56_v3.prophage-regions.bed.

2. Leave the Track category set to Region and press OK.
   
   

3. Repeat the above steps to add MG1655_m56_v3.Sigma32_regulon.bed.

*Note: Tracks can be renamed by right-clicking on their names in the Tracks panel (not in the views) and choosing Rename or Rename with Fields. This is the same basic procedure used to rename sequences in Part A of this tutorial. You can rename the tracks if you wish, but it is not necessary for this tutorial.

Now that the tracks are loaded into the session, the next step is to find regulon members that reside within prophages. One way to do this is to use the Overview to manually navigate to each of the ten prophage regions in the BED file and visually check whether any regulon regions overlap prophage regions.

4. In the Overview, move the horizontal zoom slider to the left, if it is not already there. Even zoomed out the whole way, you should be able to see 10 orange regions in the MG1655_m56_v3.prophage-regions.bed track.

5. In the Analysis view, move the horizontal zoom slider until the viewport (the semi-transparent vertical bar in the Overview) is narrower than 1 cm in width. Then drag the Viewport so that it is over the left-most orange region.
   
   
   
   In the Analysis view, adjust the horizontal zoom slider so that the entire CP4-6 prophage region is visible. Note that the regulon track below it does not contain any data at this point, indicating that there are no overlapping regulons in this region.
   
   

6. Repeat the previous step for each of the other nine prophage regions. You should see overlapping regulons at two of them.
   
   One is the fifth prophage from the left (“Qin”):
   
   
   
   The other is the ninth from the left (“CP4-57”):
   
   

7. Under CP4-57, click on the orange arrow to see the regulon member’s region name and coordinates in the Details panel.
   
   
   
   Imagine you are interested in the gene dnaK, and want to see if is a member of the regulon.

8. In the navigation area at the top of the window, start typing dnaK. As you type, a list of matches appears.
   
   
   
   You can select dnaK from the list by double-clicking on it. Or simply finish typing the name manually and press Go or Enter/Return.
   
   In the Analysis view, you can see that dnaK is indeed a member of the regulon.
   
   

Congratulations on completing the tutorial!