I analysed PPI network after integrated gene expression data from alzheimer's disease experiment within PPI network and reveals some sub network. First, I used (limma package) for Differentially Expressed Gene analysis. Second, I mapped DEG genes on the PPI network and assign the gene fold change value to corresponding proteins. Third, I search the network by selected my candidate gene and reveals sub-networks. I scored them by my formula, then I merge the top scoring sub networks.
Now, I want to validate my results (merged sub network) and I have no idea how to do.
Could anyone help me or suggested a method to validate my outcome please? I will highly appreciated
we may perform Gene Ontology enrichment analysis for specific outcome in that sub-network and correlate to the computational prediction. but before doing that we could have some clue of evidence about that specific PPI in databases like String, then we could do comparative analysis.
http://amp.pharm.mssm.edu/Enrichr/
http://amp.pharm.mssm.edu/g2e/
for enrichment analysis
We are struggling with simmilar problems. Is it really enough to do an enrichment analysis to prove the validity of your network and scoring function?
I suggest to analyse randomization of the genes in the network and the topology of the network itself as well. In any network analysis quite often you get the hubs (because they are hubs so more shortest paths are going through them) and you need to control this kind of effect. If I understood your work you did some kind of shortest path analysis with your candidate genes and Deg genes.
Dear Dr Dezső
Thanks for your suggestion
I actually capture the node degree and the network topology on my analysis approach. what I am struggling with is the validation of my outcomes. I spilt the data to training and testing. However I am not sure if using SVM and calculate the accuracy is enough for validation!
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