[BioC] identifying drosophila miRNA targets

James W. MacDonald jmacdon at uw.edu
Thu Mar 28 17:43:14 CET 2013

Hi Fiona,

I have a function called mirna2mrna (yeah, I know, lame function 
name...) in my affycoretools package that does this, based on the sanger 
microcosm targets data that you can download here:


there is also a function makeHmap() that will create a heatmap with the 
miRNA/mRNA pairs, where the color of the cells is based on the 
correlation between the two RNA species (with the intent to show 
negative correlations, indicating that the miRNA is hypothetically 
causing premature degradation of the mRNA).

I think the help pages for these two functions are reasonable, but 
please let me know if you have any questions.



On 3/28/2013 12:30 PM, Fiona Ingleby wrote:
> Hi everyone,
> I am working with mRNA data from Affy 'drosophila2' arrays and miRNA data from Affy 'mirna3' arrays. I have identified a list of differentially expressed mRNAs and miRNAs. I'm having a bit of trouble with some downstream analyses and I'm hoping someone might be able to offer some help.
> I would like to use my list of differentially expressed miRNAs to access online databases (e.g. miRBase, microRNA.org…) and extract the names of all the potential target mRNAs. Then I'd like to use this list of mRNAs to look through my mRNA expression data. I'm aware of packages like 'RmiR' and 'microRNA' which have built-in functions for finding miRNA targets, but as far as I can tell, 'RmiR' uses miRNA databases for humans only and 'microRNA' works with human and mouse data only. So is there a package I am unaware of (or another application of 'RmiR'/'microRNA' that I am unaware of) for looking at drosophila data?
> So far I have also considered the 'biomaRt' package to see if the database query function on there can help me, but I haven't had much luck. For instance, if I try an example list of miRNAs:
> mirna<-c("dme-miR-1002","dme-miR-312","dme-miR-973")
> library(biomaRt)
> ensembl<-useMart("ensembl",dataset="dmelanogaster_gene_ensembl")
> getBM(attributes="mirbase_accession",filters="mirbase_id",values=mirna,mart=ensembl)
> then 'logical(0)' is returned, as if there are no records for those miRNAs - but by searching the database manually I know the records are there.
> Alternatively I can try:
> miRNA<- getBM(c("mirbase_accession","mirbase_id", "ensembl_gene_id", "start_position", "chromosome_name"), filters = c("with_mirbase"), values = list(T), mart = ensembl)
> which returns a table of various bits of information on miRNAs, but I cannot adapt this command to just look at my list of miRNAs of interest (ie. the 'mirna' vector above). I've included the sessionInfo() output for these at the bottom of the email, but I suspect my problem is more to do with the fact I'm not going about this the right way (as opposed to a problem with package versions and coding etc.). I'm not even sure that using 'biomaRt' will give me the information I eventually want (the target mRNAs of these miRNAs), I was just trying it out, to see what it was capable of in terms of querying these databases.  So I apologise for the vagueness. Since I haven't managed to get very far by myself then it's difficult to be more specific, but I'd really appreciate it if anyone could offer some advice, even just to point me in the direction of a useful package which might have gone unnoticed by me.
> Many thanks,
> Fiona
> Dr Fiona C Ingleby
> Postdoctoral Research Fellow
> University of Sussex
> Email: F.Ingleby at sussex.ac.uk
> Website: fionaingleby.weebly.com
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] biomaRt_2.14.0     affy_1.36.1        Biobase_2.18.0     BiocGenerics_0.4.0
> loaded via a namespace (and not attached):
>   [1] affyio_1.26.0         BiocInstaller_1.8.3   grid_2.15.2           lattice_0.20-14       Matrix_1.0-11         MCMCglmm_2.17
>   [7] preprocessCore_1.20.0 RCurl_1.95-4.1        tools_2.15.2          XML_3.95-0.2          zlibbioc_1.4.0
> 	[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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