[BioC] miRNA analysis advice

[James W. MacDonald]

Hi Fiona,

On 2/25/2013 8:14 AM, Fiona Ingleby wrote:
> Dear all,
>
> I am working with microRNA data and as it is very new to me, I have some general questions. I'm hoping that some people on this list who know more about microarray analysis and miRNA than myself might be willing to offer some opinions/advice.
>
> First, when doing quality checks on the data, how useful is it to look at the RNA degradation plots with miRNA, given how short miRNAs are?

Assuming here that you have an Affy miRNA array of some sort, not useful 
at all. Note that the Affy probes are all 25-mers, and miRNA transcripts 
are 21-23 nt long. In the vast majority of cases (with mature miRNA 
transcripts; this doesn't apply to the scaRNA, snoRNA nor hp-miRNAs), 
the duplicate probes are all identical. So the underlying premise behind 
the RNA degradation plot doesn't hold.

>
> Second, when analysing differential expression (using lmFit and eBayes in the 'limma' package), I find quite high numbers of probes which are significantly differentially expressed across my samples (in some contrasts as many as ~500 out of 4000 probes are significantly differentially expressed between samples). Is this unusual with miRNA data? Further, although a lot of these probes are from Drosophila species (which I expected since my samples are from D. melanogaster), some are from other insects, and even other phyla (there are some C. elegans and human miRNA probes which are found to be significantly differentially expressed, for example).
>
>  From what I have read in the literature so far, there does seem to be some conservation of miRNAs between diverse species, but I can't find any information about to what extent I might expect to find this in my data. I'm a little concerned that this level of homology between species might be unusual, which would suggest that I've made a mistake in the analysis.
>
> As I said, I am very new to this, so if anyone is willing to offer advice or just point me in the direction of some useful information I could look at myself, then I would really be very grateful.

In general I like to see somewhere around 15-30 differentially expressed 
miRNA transcripts, as anything more can become quite intractable for the 
people I collaborate with. This is because each miRNA may target > 1000 
mRNA species, so too many miRNAs and all of a sudden every gene might be 
a potential target.

That said, I just did an analysis looking at different brain regions in 
a particular bird species and there were hundreds to thousands of 
differentially expressed miRNA transcripts, depending on the contrast.

So the fact that you have lots of differentially expressed transcripts 
doesn't necessarily mean you made a mistake. In addition having probes 
from other species pop up might not be a bad thing. In my experience, if 
you get the same miRNA from multiple species differentially expressed, 
it is because the miRNA is highly conserved, and there are little or no 
differences in the sequence.

One thing we commonly do is to start with just those miRNA transcripts 
that from the species under consideration. This can help limit things to 
a tractable number of miRNAs.

Best,

Jim


>
> Many thanks in advance,
>
> Fiona
>
> Dr Fiona C Ingleby
> Postdoctoral Research Fellow
> University of Sussex, UK
>
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099