cytoscape-STRING: customizing the evidence type used to create the create the network?

[tomer....@gmail.com]

Hi,
In the web application of STRING there's an option to choose which types of evidence should be used to create the network.

when working with the cytoscape app of STRING, I found out columns regarding the scores by each kind of evidence, but didn't find a way to use only some of them.
for example, I'd like to check what connections are there for my protein, on the basis of experiments databases, and coexpression only.

is there a way to do that?

thanks alot!
Tomer

[Lars Juhl Jensen]

It depends a bit on what specifically you want to do. What you cannot do is to turn on and off different channels and get a combined score based on only some of the channels (that is only possible through the web interface).

If you want to show only the scores from a specific channel, you can obviously change the visual style so that edge color and thickness depends on the subscore you want to see rather than on the combined score. You can also use the subscores in Cytoscape select filter to make Boolean selections based on the subscores.

However, I would also urge you to think about why you would want to turn off certain evidence channels. The scores have been carefully designed to be comparable across evidence channels, so you should not expect to get a more reliable network by turning some of them off. If you want a network with fewer false positives, the better solution is to increase the confidence threshold. The exception is if you want a physical protein-protein interaction network, but in that case you would only want to use the experiments evidence channel (so no need to combine scores).

There are situations when you want to exclude certain types of evidence for scientific reasons (e.g. to avoid circular reasoning when you combine a STRING network with some other data).

Cheers,

Lars

[tomer....@gmail.com]

בתאריך יום רביעי, 15 באוגוסט 2018 בשעה 12:00:19 UTC+3, מאת Lars Juhl Jensen:

Thanks you very much for the detailed answer. I'd definitely think about what you brought up.
best,
Tomer