I draw PPI network of my data analysis using Cytoscape CluePedia plug-in, but only about 20percent of my node were in network and lots of them weren't, then i thought of merging my network with its kinase and transcription factor network, but even with merging with these two, the result didn't change that much so lots of my node that weren't in network at first didn't come to my mreged network either, So I'll be thankful if you suggest me a method, way or anything that i can have better PPI network with little of the node out of the network.
Hi Ali,
I cannot be of much help in CluePedia plugin as I never used it but after checking the documentation as it happens with several tools the limitation is usually in the annotations, and it seems like for your network for most of your genes you dont have a PPI or functional annotation right? Have you done a network analysis to see the degree, centrality... and network stats assessment? Maybe you should center your attention in the nodes that are connected and not in the orphan ones as you have information about these ones and maybe you will be able to find something relevant.
If not as Pritam suggested, you may need to change your approach and methodology.... On that regards, what I have being doing is
1. Annotating the genes in the transcriptomics analysis with the GOs and KEEG terms using GAGE package in R
2. Selection of pathways I wanted to highlight,and the genes involved.
3. Finding all the PPI of these list of genes using several confidence thresholds in STRINGDB.
4. Representing the network in Cytoscape
5. Network analysis: to assess the features of the network
6. Further study centrality measures and nodes relevance in both Cytoscape and igraph R package
Best,
Unless there are specifically important proteins (for your specific study) amongst the 'orphan' nodes then simply discarding them for display purposes is OK - or you could try and find alternative platforms to search for additional connections, e.g. MIPS or IntAct ?
Cytoscape has a feature called Import Network from Public Databases. You can access various databases through this function, under File → Import → Network → Public Databases....
Or you can browse the respective interactions using PSICQUIC : http://www.ebi.ac.uk/Tools/webservices/psicquic/view/home.xhtml
Good Luck
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