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Protein-protein interaction database for human

Hi everyone

Do you know what is the best PPI network data base for human? I have some genes that we doubt they are related to tumor, but we need to do some more investigations? I use Biogrid, wonder if everyone uses anything else?

Thanks

protein-protein-interaction
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updated by Leite Leite • written by Dayna • Dayna

3 answers

How about STRING: functional protein association networks, which appears to be quite popular recently.

It allows you to work with your own data.

Here's a screenshot from Example 2 on the website: s

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written by Kevin Blighe Kevin Blighe

thank you so much. so people usually use a prediction db rather than a primary database from literature? I am validating my thoughts with what people do, I am a newbie :)

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written by Dayna • Dayna

Well, one can build what's called a co-expression network, which is essentially just representing correlations between your genes or proteins. In this way, for example, one can remove edges hat fall below a certain correlation threshold (like absolute Pearson r < 0.8). In this regard, I posted a tutorial here: Network plot from expression data in R using igraph

One can also use information from online databases and published literature, which is STRING's default mode of functioning.

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written by Kevin Blighe Kevin Blighe

STRING contains multiple types of interactions including physical interactions.

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written by Jean-Karim Heriche Jean-Karim Heriche

Thanks Kevin and Jean-Karim.

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written by Dayna • Dayna

For physical protein-protein interactions, I recommend working with aggregated data such as iRef index (or compiling such an aggregated data set yourself if you need something more up-to-date) as this is more exhaustive. For functional association, you can combine different types of data as for example done by GeneMANIA. For an introduction on how this works, have a look at my paper here.

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written by Jean-Karim Heriche Jean-Karim Heriche

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