Cell line information

[Denis Schapiro]

Dear Omnipath team,

Thank you for providing this awesome tool! Is there a possibility to query pathway information by cell lines?

Best regards,

Denis

[Dénes Türei]

Dear Denis,

Thanks for your question.
Most of the network resources don't have information about which interaction in which cell type has been described. Even if they had the data would be very sparse.
For the proteins pypath has two generic sources of expression data: ProteomicsDB (https://proteomicsdb.org/; mass spec data) and Human Protein Atlas (http://proteinatlas.org/; immunohistochemistry data). Using these you can remove those proteins which are not expressed in the cell type of your interest and get a network of interactions with a higher likelihood to occur in that cell type. I recently tested and fixed the code in pypath for ProteomicsDB and HPA as these were quite old parts of the module. Now it should work if you update to pypath 0.7.6 (http://pypath.omnipathdb.org/releases/). See here a basic example how to get a tissue specific network: https://bitbucket.org/snippets/deeenes/jLRBG
You can also access the expression levels as vertex attributes.

I hope it helps. Please tell us if you have further questions.

Best wishes,

Denes

[Denis Schapiro]

Dear Denes,

Thank you very much for your kind reply and examples. I will play around with it and get back to you!

Best

Denis