This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Create a network file to specie without PPI information

Hi!

I work with a specie without any PPI information, but I'd like to explore this. So, how is the best way to get that information? I've thought in Blast against A. thaliana, for example. Could anyone please help me?

Thank you so much!

cytoscape ppi network
• 1,577 views • link
updated by Leite Leite • written by aboutmb • aboutmb

1 answer

Hello, Olá aboutmb

I was working with goat proteins which is a not very studied animal, so I turned my list to similiar Bos taurus proteins which is the most studied ruminant (via uniprot) and so I built my network in STRING.

Example: You can to do is to turn your list into a list of the most studied Plant and so try to build your network by similarity. Tip: Look at the uniprot list which Plant are present, then convert your list.

Best Regards,

Leite

• 1 views • link
written by Leite Leite

To complete this answer, the general approach is to transfer interactions between orthologs (simply using best blast hits is not very reliable). You don't have to limit yourself to one closely related species.

• 1 views • link
written by Jean-Karim Heriche Jean-Karim Heriche

Thank you so much, guys! It worked!

• 0 views • link
written by aboutmb • aboutmb

Log in to answer this question.

More posts like this