Saccharomyces cerevisiae - mapping multiple genes to chromosome locations question

[Erin Bonnell]

Hello,

I have a list of genes and their chromosome locations and I would like to visually represent where they are located across the 16 Saccharomyces cerevisiae chromosomes so that they can be represented in a single figure as well as looking to see if there are any patterns in their location.  What is the best way to go about doing this? 

Thanks,

Erin Bonnell 

[Brian Lee]

Dear Erin,

Thank you for using the UCSC Genome Browser and your question about visualizing data across various Saccharomyces cerevisiae chromosomes.

We have two tools that could be of interest for this type of visualization. The first is called Genome Graphs that allows all chromosomes to be viewed annotated with signals in different locations, and the other is called Multi-Region, which allows you to slice the current browser view into multiple regions across different chromosome to be seen side-by-side.

The first step in this example will be to have coordinates in BED format that designate gene regions of interest. For example, here are some gene regions that can be pasted into our Custom Track page ("My Data" top blue bar menu, and then select "Custom Tracks") when you are viewing the sacCer3 assembly:

1. Navigate to http://genome.ucsc.edu/cgi-bin/hgCustom?db=sacCer3

2. Paste in these BED coordinates (4th column is name):

chrIV 917570 921647 YDR227W_SIR4

chrIV 376756 378445 YDL042C_SIR2

chrXI 640539 642504 YKR101W_SIR1

chrXII 1019315 1022251 YLR442C_SIR3

chrIV 378101 378455 YDL041W

With these custom tracks added you can then navigate to the "Graph Genomes" tool ("Tools" top blue bar menu and then "Genome Graphs").

3. Click the "Import" button. 

4. Change the "group:" to "Custom Tracks" 

5. Enter a name like "spots" in the "name of the data set".

6. Click "submit" and then "Go".

7. Now load this new set by go to the "graph" menu and change it from "--nothing--" to "spots1" and you should see an image like this one saved from a session where these steps were taken: http://genome.ucsc.edu/cgi-bin/hgGenome?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=sacCer3_spots

Note that you can click this graph image (for example peaks) to jump to the regions of interest.

The second approach uses our Mulit-Region Tool. When viewing the sacCer3 browser (http://genome.ucsc.edu/cgi-bin/hgTracks?db=sacCer3) and using the same BED coordinates that you used to make a custom track. First go to the "View" menu in the top blue bar and select "Multi-Region".

In the bottom box paste the same information you used to create the custom tracks:

chrIV 917570 921647 YDR227W_SIR4

chrIV 376756 378445 YDL042C_SIR2

chrXI 640539 642504 YKR101W_SIR1

chrXII 1019315 1022251 YLR442C_SIR3

chrIV 378101 378455 YDL041W

Then click the radio button next to the box to use these "Custom regions as BED" and also click the checkbox on the "Highlight alternating regions in multi-region view" option and then click "submit" to return to the Browser.

You will now be zoomed in on one of the regions (these regions will slice depending on the order they were entered). Zoom out 100% and you will now be seeing the entire region with a session like the following: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=sacCer3_spots

Note that the far left side represents the small chrIV YDL041W item, that overlaps with the YDL042C_SIR2 item. This helps emphasize how the order of the coordinates are entered into multi-region determines the final view, it also explains why in the Genome Graphs view only 4 peaks display for the five items, as two of the items overlap.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UC Santa Cruz Genomics Institute

Training videos & resources: http://genome.ucsc.edu/training/index.html

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Host a workshop: http://bit.ly/ucscTraining

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