Question: what does miRNA* mean?
1
gravatar for l0o0
3.7 years ago by
l0o0210
China
l0o0210 wrote:

I am reading a paper about miRNA and confused by a fig. enter image description here

In "Novel miRNA for which miRNA* were found", what does miRNA* mean in the context? Does it mean reverse-complement sequence of miRNA?

I hope someone could give me some suggestions.

mirna • 1.5k views
ADD COMMENTlink modified 3.7 years ago by Michael Dondrup47k • written 3.7 years ago by l0o0210

The asterisk refers to the line at the bottom of the image, "*Known miRNAs refer to..."

ADD REPLYlink written 3.7 years ago by Brian Bushnell17k

That is misleading within this figure, they should have used a different character.

ADD REPLYlink written 3.7 years ago by Michael Dondrup47k

The * points to the clarification at the end of the figure. I quote:

*Known miRNAs refer to miRNAs with <=2 mismatches to miRNAs deposited at the miRBase v20."

That is, from the "novel miRNAs" some are similar to "known miRNAs" (according to the criteria specified in *).

ADD REPLYlink written 3.7 years ago by ddiez1.9k
3
gravatar for Michael Dondrup
3.7 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

miRNA* refers to the antisense sequence to the mature miRNA. miRDeep classifies miRNA reads based on the location of reads in the pre-miRNA: miRNA (mature miRNA sequence), miRNA* (as sequence of miRNA), and loop (matching loop region of pre-miRNA hairpin).

ADD COMMENTlink written 3.7 years ago by Michael Dondrup47k
2

It's a bit deprecated these days and miRNAs are referred to as 5'-miRNA and 3'-miRNA since it was hard to determine which side is the active one.

ADD REPLYlink written 3.7 years ago by Asaf8.4k

Oh, I see. Missed that detail (not familiar with miRDeep). Would you please provide a link where this is documented/explained? Thank you.

ADD REPLYlink written 3.7 years ago by ddiez1.9k

Check out the documentation or check the PDF generated for each Mirna. There they use the same notations

ADD REPLYlink written 3.7 years ago by Michael Dondrup47k

Thank yourfor your answer. In my mind, novel miRNAs seem to be not in the miRbase but they have a miRNA-like structure. Is it necessary to check miRNA* for novel miRNA?

ADD REPLYlink written 3.7 years ago by l0o0210
  • Sure, novel miRNA are not in any database. However, if you don't provide mirDeep2 with information on known miRNA, it will summarize all detected miRNA as 'novel'.
  • running mirDeep alone is not sufficient to classify short RNA into miRNA, and other small RNA. Running cmscan (earlier Rfam_scan) is a good way to get additional annotation information.
  • The mirDeep algorithm does check for miRNA, miRNA*, and loop; and counts the numbers of reads mapping to either. I think that the expectation is that miRNA should get the highest number of reads, because of how the miRNA is integrated with RISC. If detecting miRNA de-novo, this helps to determine which part of the stem of the hairpin is used.
ADD REPLYlink modified 3.7 years ago • written 3.7 years ago by Michael Dondrup47k
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