Gene-Gene interaction expression analysis

Question

[Payton Yau]

I am looking for some R packages for gene-gene interaction analysis.

Are there any tools which allow me to select one gene as a indicator ( a central indicator for the network) from a microarray dataset (for example: 100 patients with 20000 genes) for the gene-gene interaction analysis?

Thanks,

Answer 1

[Bioaln]

This is the GO-TO in this field. What is the definition of an indicatior in your case?

Answer 2

[mforde84]

Maybe something like a multiplicative aracne network?

library(parmigene)
mat <- matrix(rnorm(1000), nrow=10) 
mi  <- knnmi.all(mat)
grn <- aracne.m(mi, 0.15)

There's an additive model as well, though the multiplicative model will presumably identify epistatic regulation(s).

There's alot of options available to you like the previously suggested WGCNA analysis, which I believe is correlative in some sense. WGCNA is common for identifying coexpressed "gene programs". Basically, it calculates the distances betweens genes expression values then groups them according to where they split on a dendrogram. It's a little arbitrary where you cut the dendrogram though, and there's no real guarantee that there is a bonfide regulatory interaction between genes within gene programs. Though it seems likely to some extent that genes with similar function or within close proximity to one another in terms of signaling cascades would be correlated to some degree greater than chance.

[Payton Yau]

Thanks for your reply. I think this is my starting point to play with. Do you know about the EGAD package?

[mforde84]

Sorry, I haven't worked with it previous. Looks pretty cool. Will definitely play around with it though. :)