Hi, I'm trying to predict interactions between certain miRNA and a lncRNA in human. I started selecting certain miRNAs that interact with some genes I was interested into. Now I pooled the results from many tables of targetscan and I ended up with a list of miRNA families. I want the sequences of miRNA to check for possible interactions with the lncRNA sequence with some online tools.
Now for example I have in my list family "miR-199-3p", if I go on the family page on targetscan I get many miRNA related to this family, which should I choose among these to check for interaction prediction? Some of these are like 199a-3p, 199b-3p and as I got the letters define abundance of these molecules in experimental settings so I am tempted to use only the "a" but maybe someone has a better principle.
Beside that there are also many other miRNA in these families, in the example above there is also mir-3129-5p that sounds a lot different and many others.
Finally there is also some family with their names separated by slashes e.g. miR-25-3p/32-5p/92-3p/363-3p/367-3p, should I check for every miRNA belonging to this group?
Thanks in advance
miRNA nomeclature is a bit messy. hsa-miR-199a-3p and hsa-miR-199b-3p are probably homologues, so they will probably share their seed sequence. You can assume they will therefore share the same targets. Check in mirbase to see their sequences, and targetscans also highlights their seed regions and can give information on the type of interaction. A further check would be to identify from where they are sequenced - i.e. introns of related genes or on the same gene.
As for miR-25-3p/32-5p/92-3p/363-3p/367-3p - it sounds like a miRNA family but I am not familiar with this one. Again just check if they have the same seed sequences. If they do, then they probably have redundant functionality.
It may be worth investing in learning a tools such as multimiR or miRNAtap - both are R/Bioconductor packaged. With them you can handle your research more automatedly. Will have to check if they can handle longnoncodingRNAs though.