Large differences in Differentially expressed genes between two datasets.

Question

[rijul]

I'm trying to identify prognostic biomarkers for early-stage Parkinson's Disease (PD) and infantile Autism Spectrum Disorder (ASD) using network system biology approach. so i have taken two GEO datasets for both of the disorders, and after differential gene expression analysis using limma I'm getting approx 1776 degs of PD and 91 degs of ASD, how to proceed further with such a broad difference among the genes, and how to move further in STRING to generate the PPI network.

Answer 1

[Scooter]

Greetings,

It's not clear to me exactly what you're trying to achieve. Are you looking for overlap between the two diseases or just looking to create two PPI networks that are independent. I'm going to assume the latter for right now. The steps are actually relatively straightforward, and we've even got a pretty good step-by-step tutorial that covers almost exactly that use case: RNA-Seq Data Network Analysis Basically, the steps are simply to take the set of genes that are differentially expressed, and paste them into the stringApp to get your network. You can then import your fold change information and p-values into the network and use that to style the nodes. The tutorial provides a much more detailed step-by-step workflow for you.

-- scooter