Draw Karyotype For A Subset Of Genes

Question

[tomislav.ilicic]

Hey,

Following situation. I have a set of genes (Mouse Ensemble IDs) and I want to colour the regions on the mouse karyotype that are in my set of genes.

Can anyone tell me if there is a straightforward way to see where all those genes in the genome belong to and then to colour those regions in the karyotype?

I am sure that something exists which does exactly that, but I just can't find it on google (maybe I look wrong)!

However, I would be really grateful for help.

Best, Tomi

[Pierre Lindenbaum]

duplicate of Drawing chromosome ideogams with data ?

Answer 1

[Emily]

You can view them in Ensembl. Go to http://www.ensembl.org/index.html and click on the mouse, then on the karyotype icon.

You can now add data. Click on "Add your data" or "Manage your data" (you'll get different options depending on whether you've already uploaded stuff to Ensembl). Choose "Features on Karyotype. Paste your list of IDs into the box then click "Show features".

You'll now see the position of your IDs indicated by little red arrows. If you don't like the red arrows, there are display options that you can change when you upload, such as different colours or displaying as lines or boxes.

You'll also get a nice little table underneath with information about your genes, such as location, name and description, and you can click on the IDs to get more information.

Answer 2

[tomislav.ilicic]

Thank you, this helps a lot!