visualizing and interpreting PPI Networks

[chris Jhon]

Hi All,

I have few protein-protein interaction (PPI) networks from different experimental conditions ,each contains about 1000 proteins ,i would like to find differences between these networks ,when i get differential networks each network contains few hundreds of proteins which is not easy to analyze by eyes , when i used MCODE i can got modules which contains only few nodes ,I would like to know how to analyze and visualize the differences between these big  networks and how to  interpret differences between different networks???

Thank you for you help in advance.
Best Regards,
Chris

[anu rupa]

hiii,

if you have to identify the differences use advanced networkmerge plugin. in that u will find an option to intersect the networks. the result will give you the commonly present proteins in all networks. all those which are not present in the result are those which are present specifically for individual networks. hope this would help you.

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anurupadevi

M.Tech Bioinformatics

karunya university

8886953046

[chris Jhon]

Hi Anu,

Thank you for your kind help.
I have tried that already and got networks of few hundreds.
imagine now i have 4 networks each with about 700 nodes which are the result of using the tool you explained ,i would like to visualize and interpret the significance of this results but as networks are relatively big ,i would appreciate any suggestion.

Thank you

[Vijayaraj Nagarajan]

One of the things you could do;
You could take the list of proteins from these individual networks, run them through DAVID and use the enrichment map plugin to visualize the DAVID data in cytoscape.

http://david.abcc.ncifcrf.gov/
http://baderlab.org/Software/EnrichmentMap/DavidTutorial

-Vijay

[chris Jhon]

Hi Vijay,

Thank you very much for kind help.
I have already done that but i got a network for also few hundreds GO terms for each network which i can't analyze by eyes.even when i tried to get the unique terms that exist only in a certain network i got a few hundreds GO terms,so ,is there a standard way to analyze such networks.

Any help is appreciated
Chris

[Vijayaraj Nagarajan]

Hi Chris,

Not sure if you tried the top levels in the GO hierarchy. The top levels should help bring down the numbers.
A strict pvalue could also be used to filter further.

-Vijay

[chris Jhon]

Hi Vijay,
Thank you again for your kind help.
May i ask you how to confirm whether i'm using top level GO terms or not.I'm using DAVID to get GO terms.
I really appreciate your help.
Thank you

[Vijayaraj Nagarajan]

Hi Chris,

By default DAVID selects the ALL option for the GO.
You can uncheck everything else (using the "clear all" button that is present in the right hand side corner) from the list and then check only the top level of GO (for example the GOTERM_BP_1) as shown in the screenshot below.
This should give you relatively low number of hits.

Hope this helps.

Cheers,
Vijay

[chris Jhon]

Hi Vijay,

Thank you very much.

Best Regards,
Chris.