miRNA microarray - mature and minor miRNA forms - (Jul/20/2008 )
I am quite new in the miRNA field and are therefore lacking a lot of background.
At the moment I am analyzing the results form a miRNA microarray which is why I have some questions;
First, how can it be that the minor form of a miRNA is up- or downregulated but the major form is not? As both derive from the same transcript shouldn't then both forms behave in the same way? Or can it be, that although there is more transcript, the levels of RISC incorporated major form stay the same, but the levels of RISC bound minor form increase? I must say I do also not no at which step the hybridization occurs - the pre-miRNA level or the post Dicer level?
Also I would like to ask you, what you use for target prediction. So far I am mainly using the target predictions from the sanger site but I read that many people recommend the miRANDA software so I tried it too. I downloaded all human 3'UTRs form ensemble and run them against my miRNA of interest. But then I get this long list which I can not sort according to the score and also the gene name is not indicated, so I have to look up every ensemble ID for the corresponding gene name.
I would be grateful for any advice
I don't know about the levels of expression. For the prediction of targets you could use this paper to get an idea. NATURE METHODS | VOL.3 NO.11 | NOVEMBER 2006 | 881