Question: Protein protein interaction network using STRING
0
gravatar for Leite
3.0 years ago by
Leite410
Leite410 wrote:

Hello everyone!

I'm creating a protein protein interaction network in STRING (http://string-db.org/) with 110 proteins, but appeared some doubts.

1. What "minimum required score interaction" use?

I made my network with> 0.400, but found papers that use> 0.700, already one with> 0.150.

Ai came the question, what "minimum required interaction score" should I use?

2. Use or not use the "textmining"?

I saw in some papers, researchers removing this option.

Ai came the question, what options I should keep?

3. Can I do search only one protein in string (max number of interactors to show: 1st shell: no more 10) and then do the merge in Cytoscape with the network? That is correct? or was manipulating my data?

The aim is to know the interactions of each of the 110 proteins and how they interact with each other and so on.

ADD COMMENTlink modified 3.0 years ago by Girolamo140 • written 3.0 years ago by Leite410
0
gravatar for Girolamo
3.0 years ago by
Girolamo140
Italia
Girolamo140 wrote:

1 and 2) these two questions are correlated. This affects the reliability of your network. I would remove text mining and the other options, and leave only those interaction experimentally validated with a threshold > 0.700. 3) do you want to do it routinely for all the 110 proteins? this could take ages :-)

ADD COMMENTlink written 3.0 years ago by Girolamo140

Thank you very much Girolamo

ADD REPLYlink modified 2.0 years ago • written 3.0 years ago by Leite410
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