Question: miRNA-Target coexpression and network
gravatar for Prasad
3.4 years ago by
Prasad1.6k wrote:

Hello, i have miRNA data for 4 samples (plant whose genome is not available) and have corresponding predicted targets. I have the following queries.

  1. What is the way to the co-expression analysis between miRNA and its targets.
  2. How to generate the miRNA and target network based on the expression data

Any suggestions. Thanks

mirna network gene • 1.3k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Prasad1.6k

I think this is really going to be a bit difficult, and you will need a bit more than the 4 miRNA samples. I think first step is to find out if you have sufficient data at all and if it is worth doing the analysis. So you would need: assembled transcripts, seems like you have them because have predicted targets. You definitely also need RNA-seq data, you also mention expression data, would optimally be replicated.

The simplest way of determining co-expression between miRNA and target is based on correlation (target expression should be negatively correlated with miRNA expression in theory), as is the construction of a co-expression networks. The downsides are in my opinion, the target prediction for miRNA is really noisy with many false positives, and it is not clear if RNA-seq can capture well the post-transcriptional regulation by miRNA. In addition, I am assuming that the 4 samples also were used to predict miRNA's de-novo, now these should be re-used for differential expression analysis. The whole setting bears very little foundation in validated structural features (de novo genes/transcripts, de novo miRNAs, de novo targets for these, gene expression analysis using the same data used to build transcripts and miRNA). I think we could pull up a few papers arguing for either position.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Michael Dondrup46k
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