.phos file input for PhosphoPath

[Shivangi Awasthi]

Hi all,

So I followed the manual for the PhosphoPath app and it worked fine. I am trying to use the app on my phosphoproteomics data. I wanted to know how can i generate the .phos file for network input like the "dataset.phos" file from the tutorial. Thanks so much!

[Barry Demchak]

Hi --

Forwarding your question to the app authors for direct assistance.

... please stay tuned.

On Tue, Mar 14, 2017 at 1:01 PM, Shivangi Awasthi <shiva...@gmail.com> wrote:

Hi all,

So I followed the manual for the PhosphoPath app and it worked fine. I am trying to use the app on my phosphoproteomics data. I wanted to know how can i generate the .phos file for network input like the "dataset.phos" file from the tutorial. Thanks so much!

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: Barry Demchak, PhD
: UC San Diego, Department of Medicine
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[Rubin joshi]

I created a tab delimited text (.txt) file in the exact format as the example dataset in R. Then I just changed the extension to .phos from .txt. Then it works. The only issue I had was if I used excel to do the reformatting cytoscape only accepted the first protein. It is probably because reformatting with excel might tamper with the text separator (maybe). But as long as I used R to do everything, it worked.

Cheers,

Rubin