Question: How to build a protein-protein interaction network?
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gravatar for Leite
3.2 years ago by
Leite1.1k
São Paulo - Brazil - Unifesp
Leite1.1k wrote:

Hello everyone,

I would like to know if there is a correct way to build an PPI network.

Examples I've seen in articles

  1. Download all the interactions of the HPRD or BioGRID and open in the cytoscape, searches for the all seed interactions at once, and then creates a new network.

  2. Searches for the seed interactions one by one in STRING, BioGRID, Reactome and then merge all in Cytoscape.

Best Regards,

ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 3.2 years ago by Leite1.1k

you can also use biomaRt, i.e pathwaycommons and Paxtools

ADD REPLYlink written 3.2 years ago by jaslibra10

So, I think biomaRt is another away to do that. But what I need to know is how the best away to construct one PPI. 1. Using all seed at once,based on an interactome HPRD or BioGRID. or 2. Searches for the seed interactions one by one in STRING, BioGRID, Reactome and then merge all in Cytoscape.

ADD REPLYlink written 3.2 years ago by Leite1.1k
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