[BioC] identifying drosophila miRNA targets
James W. MacDonald
jmacdon at uw.edu
Fri Mar 29 19:30:08 CET 2013
It's not you. The function is set up with the assumption that you will
be using ensembl data, not flybase. I'll take a look and see if I can
make the requisite changes.
On 3/29/2013 8:09 AM, Fiona Ingleby wrote:
> Hi Jim,
> Thanks very much for pointing that out - it seems mirna2mrna is
> exactly what I was after, I don't know how I managed to overlook it….
> I'm a bit puzzled about the results I'm getting, however, and so if
> you have a minute to think this through then I'd be really
> grateful. The help pages are pretty clear, and so I've managed to get
> the function to run with my data without any problems….but I'm getting
> 'named list()' as output. Which might simply suggest that there are no
> correlations between the miRNAs and mRNAs in my data (?). But I'm not
> convinced and I'm wondering if I've done something wrong somewhere
> along the way (I'm looking at 39 differentially expressed miRNAs along
> with 2638 differentially expressed mRNAs, so I'd be surprised if there
> were none that correlate with each other).
> I'm wondering if I'm doing something daft like using RNA IDs in the
> wrong format (which might be one explanation for getting 0 matches
> returned from the database?). At the moment I'm just taking character
> vectors directly from the ExpressionSet. So I have 2 ExpressionSets,
> each representing only the probes which are significantly
> differentially expressed in each dataset - I've called these sigmRNA
> (2638 x 12 samples) and sigmiRNA (39 x 12 samples) for mRNA and miRNA
>  "1622906_at" "1622915_at" "1622917_a_at" "1622920_at"
> "1622926_at" "1622932_s_at" "1622935_at" "1622940_at" "1622946_at"
>  "1622952_at" "1622956_at" "1622959_at" "1622960_at"
> "1622965_s_at" "1622974_at" "1622975_at" "1622978_at" "1622992_at"
>  "1623002_at" "1623004_a_at" "1623008_at" "1623019_a_at"
> "1623022_at" "1623025_at" "1623026_a_at" "1623030_at" "1623031_a_at"
> …and so on for 2638 entries.
>  "dme-miR-1002_st" "dme-miR-1004_st" "dme-miR-1017_st"
> "dme-miR-124_st" "dme-miR-2500_st" "dme-miR-286_st"
>  "dme-miR-2a_st" "dme-miR-306_st" "dme-miR-310_st"
> "dme-miR-311_st" "dme-miR-312_st" "dme-miR-313_st"
> …etc. So I'm using mirna2mrna like this:
> miRNAannot="v5.txt.drosophila_melanogaster", #downloaded from the
> rbi website and saved in the working directory
> and then I get:
> > test
> named list()
> I've put the sessionInfo() output at the bottom of the email. I also
> looked through the source code on the Bioconductor code search
> website, pulled out the 'convertIDs' function, and ran this as an
> independent function on the lists of RNAs to check to see what it was
> doing, but I can't see anything that looks odd to me - it removes the
> '_st'/'_at' as I expected.
> So I'm a bit stuck. I'm sure I've misunderstood something, but can't
> pick out what it is myself. I suppose it's totally possible that the
> analysis is fine and there are just no correlations between the miRNAs
> and mRNAs of interest in my data - but I thought I would check. If you
> (or anyone) has any ideas, I'd really appreciate the help.
> Thanks again,
> Dr Fiona C Ingleby
> Postdoctoral Research Fellow
> University of Sussex
> Email: F.Ingleby at sussex.ac.uk <mailto:F.Ingleby at sussex.ac.uk>
> Website: fionaingleby.weebly.com <http://fionaingleby.weebly.com>
> Tel: +44(0)1273678559
> > sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  drosophila2.db_2.8.1 org.Dm.eg.db_2.8.0 RSQLite_0.11.2
> DBI_0.2-5 AnnotationDbi_1.20.7 Biobase_2.18.0
>  BiocGenerics_0.4.0
> loaded via a namespace (and not attached):
>  IRanges_1.16.6 parallel_2.15.2 stats4_2.15.2 tools_2.15.2
> On 28 Mar 2013, at 16:43, James W. MacDonald <jmacdon at uw.edu
> <mailto:jmacdon at uw.edu>> wrote:
>> 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:
>>> 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,
>>> Dr Fiona C Ingleby
>>> Postdoctoral Research Fellow
>>> University of Sussex
>>> Email: F.Ingleby at sussex.ac.uk
>>> Website: fionaingleby.weebly.com
>>> R version 2.15.2 (2012-10-26)
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>>> attached base packages:
>>>  stats graphics grDevices utils datasets methods base
>>> other attached packages:
>>>  biomaRt_2.14.0 affy_1.36.1 Biobase_2.18.0
>>> loaded via a namespace (and not attached):
>>>  affyio_1.26.0 BiocInstaller_1.8.3 grid_2.15.2
>>> lattice_0.20-14 Matrix_1.0-11 MCMCglmm_2.17
>>>  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]]
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
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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
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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