Question: protein interaction database
3
gravatar for yliueagle
5.4 years ago by
yliueagle220
France
yliueagle220 wrote:

I want to utilize protein-protein interaction knowledge (Human) for my analysis. I find there are many databases provide such information, such as BioGRID, STRING, HPRD, PINA. The problem is that the interaction information from these databases differ a lot. For example by querying APP, it returns 1975 interactors from BioGRID, while by STRING only 10 interactors. Another example that querying ZPBP2 it returns 10 interactors from both BioGRID and STRING, but with 0 overlap. For those who have experience in protein interaction analysis, can you provide some suggestions?

Thanks.

 

database protein interaction • 2.1k views
ADD COMMENTlink written 5.4 years ago by yliueagle220
2

Re STRING, try changing the drop-down from 'no more than 10 interactors' or add a custom limit to the number of interactors you want to see.

ADD REPLYlink written 5.4 years ago by russhh5.1k
2

just a general comment: with STRING you get always 10 interactors, since the default behavior is to only show the top 10 interactors. you can change this at the bottom of the page. you can also decide to show interactions based on how they were determined (experiments, databases, text-mining). you can read about this in the help page.

ADD REPLYlink written 5.4 years ago by Martombo2.6k
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