Methods of looking at miRNA target enrichment in lists of genes

Question

[james.os]

Hi,

I'm trying to figure out what the best way of doing this analysis is, or if anybody knows any good R packages.

So basically I've got RNA-seq results for gene and miRNA expression. I've got 3 conditions in the study (3 different groups), and I've already done my analysis to find significantly differentially expressed genes and miRNA between each of the groups.

Simplistically, my groups are: (1) Sham surgery, (2) surgical model of disease at 7 days post-surgery, (3) surgical model of disease at 14 days post-surgery. Based on this, I've made a number of lists of genes/miRs based on their expression profile in each of the 3 conditions, for example: significantly increases between 1 and 2, then significantly decreases between 2 and 3. So the analysis I want to do now is: predict the targets of the miRNA and look for enrichment of these targets in the complimentary gene expression list. In other terms, I want to assess how miRNA expression changes may be influencing the transcriptomic profile.

Any ideas?

Answer 1

[i.sudbery]

I recommend looking at Sylamer, it looks for enrichment of miRNA seed sequences in the UTRs of genes which are ranked by their change in differential expression analyses.