I would like to infer the gene network from the gene X to its secretome. I've a RNAseq DEG analysis (gain of function for the gene X), and also the secretome of this gene.
Using the differentially expressed genes from my DEG analysis as a signature I have been able to split in two cohorts (by significant survival) patients from a TCGA tumor. I took those two cohorts together (~120 patients) and used Aracne-AP to infer the gene network.
Then with this gene network model I selected the shortest paths from the gene X to the all the available genes in the secretome, then remove all the genes that were not differentially expressed in my RNAseq
Then I performed an enrichment analysis on the intermediate genes (those that are not the secretome genes), I saw that the intermediate genes are enriched in some immune genes. Then performed an enrichment analysis on the secretome genes downstream theses specific genes, and I saw that these secretome genes are enriched in some interleukines.
So far it seems that the model created by Aracne somehow reflects our hipotesis, our gene X promotes changes in immune context throughout its secretome.
I would like to refine this network to understand better the mechanism in between the gene X and its secretome, but so far I'm stuck as I don't know what to do.
Anyone knows what I could do? I'm checking other methods for network inference. Not sure what would happen if from the original TCGA data I would only used thos differentially expressed from my RNAseq to infer the network.
Thanks for your help and time.