Question: Gene-Gene interaction expression analysis
0
gravatar for tungon
18 months ago by
tungon0
tungon0 wrote:

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,

rna-seq • 630 views
ADD COMMENTlink modified 18 months ago by mforde841.2k • written 18 months ago by tungon0
0
gravatar for Bioaln
18 months ago by
Bioaln300
France
Bioaln300 wrote:

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

ADD COMMENTlink written 18 months ago by Bioaln300
0
gravatar for mforde84
18 months ago by
mforde841.2k
mforde841.2k wrote:

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.

ADD COMMENTlink modified 18 months ago • written 18 months ago by mforde841.2k

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

ADD REPLYlink written 18 months ago by tungon0

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

ADD REPLYlink written 18 months ago by mforde841.2k
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