Question: Gene-Gene interaction expression analysis
0
gravatar for Payton Yau
3.5 years ago by
Payton Yau10
Nottingham
Payton Yau10 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 • 1.2k views
ADD COMMENTlink modified 3.5 years ago by mforde841.3k • written 3.5 years ago by Payton Yau10
0
gravatar for Bioaln
3.5 years ago by
Bioaln340
France
Bioaln340 wrote:

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

ADD COMMENTlink written 3.5 years ago by Bioaln340
0
gravatar for mforde84
3.5 years ago by
mforde841.3k
mforde841.3k 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 3.5 years ago • written 3.5 years ago by mforde841.3k

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

ADD REPLYlink written 3.5 years ago by Payton Yau10

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

ADD REPLYlink written 3.5 years ago by mforde841.3k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2475 users visited in the last hour
_