Question: PIN or PPI Network Construction
0
gravatar for Pranavathiyani G
16 months ago by
Pondicherry, India
Pranavathiyani G180 wrote:

How to construct a PPI network for whole proteome of an organism? Is it possible to construct all protein interaction network? Kindly provide your suggestions.

Thank you.

ADD COMMENTlink modified 12 months ago by Emre70 • written 16 months ago by Pranavathiyani G180
1
gravatar for Jean-Karim Heriche
16 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche15k wrote:

The standard approach is to transfer existing interactions data by orthology i.e. two proteins in your target organism are linked if their orthologs in some other organism(s) have been found to interact.

ADD COMMENTlink written 16 months ago by Jean-Karim Heriche15k

If I remember correctly, string (http://string-db.org/) already adopts this approach.

ADD REPLYlink modified 16 months ago • written 16 months ago by Girolamo140
1
gravatar for Emre
12 months ago by
Emre70
United States
Emre70 wrote:

Cross-post adapted from my answer to this question:

You can find a rather outdated list and comparison of tools for interaction data integration & analysis on the Table 2 of this article, which presents BIANA, a tool for biological interaction and network analysis. (Disclaimer: I contributed to the development of BIANA.)

There is a web server version of BIANA, where you can query providing all proteins in the organism (e.g. from UniProt or ENTREZ). You can specify which types of interactions you want to include while building your network such as including only physical protein interactions produced by certain experimental techniques.

Omictools also has several relevant categories (see ppis and ppi-prediction) where you have a more up-to-date list of available tools.

Unless the species you are working on is understudied (not many known interactions), I dont think you need to use orthology information. Nonetheless, if you do want to incorporate interologs (interactions predicted by orthology), you can select "Add Interologs based on COG" option on panel 3 "Network options".

ADD COMMENTlink written 12 months ago by Emre70
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