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I would like to know what i should use to be able to build a PPI network. I have seen different structure for different techniques. for example sometimes the input look like this , each protein with another protein and a relationship 

YAL011W YBR231C 0.804967
YAL011W YDR190C 0.790977
YAL011W YDR334W 0.840367
YAL011W YDR485C 0.815874
YAL011W YJL081C 0.574536

or sometimes I only see this 

YAL011W YBR231C 
YAL011W YDR190C
YAL011W YDR334W
YAL011W YDR485C
YAL011W YJL081C

what do I need to make a network ? and which structures normally used for making these networks.

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  • $\begingroup$ What does PPI Stand for? Google UK suggests Payment Protection Insurance. Please avoid abbreviations in titles and define them in questions. $\endgroup$
    – David
    Jul 5, 2016 at 18:48
  • $\begingroup$ @David sorry david , it stand for protein protein interaction $\endgroup$
    – Nik
    Jul 5, 2016 at 19:09

1 Answer 1

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If you are asking solely about data structure, the two data formats that you have given are essentially the same. Each row represents a PPI, so in a network a line (edge) will link the proteins (nodes) given in columns one and two. Column three is an edge score, but it can indicate a few things, confidence in the interaction or strength of the interaction. Your network will for a single central node with 5 nodes linked to it in a wheel shape.

PPI networks may also be represented in Proteomics Standards Initiative Molecular Interaction XML Format. This provides a controlled vocabulary for programmatic access to data.

The choice of data structure, there are many, is yours but simple formats (as above) are often sufficient. It is important to be mindful of the meaning of the network, are the PPIs directional? Do you have estimates of interaction (edge) confidence? Do you have estimates of interaction (edge) strength?

Cytoscape will allow you to visualise a protein-protein interaction network (PPI) such as the two that you have given. The Bioconductor project provides a number of options for the visualisation and analysis of PPI networks in R.

If you want to create or build a PPI network from a single protein or list of proteins then Cytoscape, and possibly plugins such as Genemania, can also do that.

String is also useful for building PPI networks. The developers have focussed on a wide-range of species and their data export options will allow you to see the same network in a variety of data formats.

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  • $\begingroup$ your answer was great , I really appreciate it, Let me ask you a question, I have identified a list of proteins lets say 100, then if i go the String , it gives me a network, but I have no idea how it is built. Lets put it in this way, would you mind to give me a small example of if one has (as an example) 10 proteins ID, how he can reach to a network ? I already liked your answer , thanks $\endgroup$
    – Nik
    Jul 6, 2016 at 7:42
  • $\begingroup$ It's somewhat complicated but the creators of String have published a number of papers which describe how the database was assembled. If you want to know about individual interactions clicking on an edge provides that information. $\endgroup$
    – Michael_A
    Jul 6, 2016 at 8:11
  • $\begingroup$ I have read many of them, I think it is like a black box, they normally work with physical interaction but not easy to understand :-) . can you give me an example using Cytoscape then ? do you know what I want to know? I want to know how to make the structure ready to be used for PPI network . this is all what I want to know . $\endgroup$
    – Nik
    Jul 6, 2016 at 8:16
  • $\begingroup$ If you are viewing a network on the string webpage clicking on the evidence pane below the network window provides a basic description of each evidence type. If you want a file of interactions to work with; Tables/Exports > "as simple tabular text." will provide a file that can be imported into Cytoscape, the first two columns are your interactions, import those first. Cytoscape provide good tutorials. Have a try and maybe ask another specific question if you get stuck? Goodluck. $\endgroup$
    – Michael_A
    Jul 6, 2016 at 8:28
  • $\begingroup$ ok thanks, I asked as a second question biology.stackexchange.com/questions/48624/… $\endgroup$
    – Nik
    Jul 6, 2016 at 8:34

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