ceRNA identification for miRNA

[utomek]

Hello everybody,

my name is Thomas and I´m working with NGS-data.

We did a RNA-Seq of a ES-cell line with and without knock out of a specific gene. We know that there is an important miRNA which is upregulated in our experiment but the miRNA-targets do not change. So we think their might be a regulation of the miRNA by ceRNAs. But I really have no clue how to find out if I have a enrichment of ceRNA in the KO or WT experiment.

Is there a tool to answer this question or does anybody have an idea how to solve this "manually" using blast or something else.

Thank you for you help!

Best wishes,

Thomas

[andreaventura]

Hi Thomas, before looking into ceRNAs: how much is your miRNA deregulated? how abundant is its expression? Did you generate ecdf plots of the logFC of predicted targets for your miRNA?

In my experience you can easily see an effect on predicted targets only with abundantly expressed miRNAs (top 30 or so in a given cell). Also, the effects are rather small, with most of the genes showing less then 1 log2FC (up or down, depending on the direction of the change in miRNA levels).

Hope this helps.