PhosphoPath: import of quantitative data on phosphosites

[Anja Billing]

Hi,

I am using CytoScape v.3.3.0. I am trying out the PhosphoPath app using the test data set downloaded from GitHub. All works as described in the manual except the import of the quantitative data for the phospho sites. After following the steps of the table import (select the nodes, add bar of time points (2), Import-Table-File- regulation_2_tp.txt , see attachment) the ratio column in the Edge node table stays empty.

Any suggestions?

Regards,
Anja

[Linsey Raaijmakers]

Hi Anja,

From the image I can see that you put a 2 in the textbox, but didn't click the 'add timepoint bar' next to it. If you click this before you import the quantitative information, it will add these timepoint bars to the network. I don't see them in your network now.
I do have to say that the nodes in your network are very close together. Adding the timepoint bar here would probably make it very messy.
It would be better to create a subnetwork first of one or multiple pathways, or drag the nodes a bit apart first.

Let me know if you face other problems!

Linsey

[Anja Billing]

Dear Linsey,

Thank you very much for your help!
That was indeed the problem. Quantitative information per phosphosite per time point is now available.

Anja

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