[BioC] human miRNA predicted/validated targets

[James W. MacDonald]

Hi Ranjani,

On 7/8/2013 4:04 PM, Ranjani R [guest] wrote:
> Hi,
> I am hoping to find an R package/downloadable resource for validated (and predicted) miRNA targets. I have already investigated a few sites : miRWalk (which is not downloadable in its entirety and has a limit on the number of miRNA you can feed into it's web form), tarBase (which does not seem to have been updated in a while) and miRecords. miRecords does have a downloadable excel spreadsheet with validated target information (and pubmed ID) - and has 2112 miRId ->  Gene pairs.
> Which is usually the methodology of choice for working with predicted/validated targets? I am concerned with using resources that may not be updated regularly -- or in downloading a file which may be a snapshot at a certain time.

I am not sure exactly what your point here is (aren't all annotation 
data by definition a snapshot in time?). But in general BioC is released 
every 6 months, and I would in general expect the various annotation 
data to be updated as well. However, all the annotation in BioC are just 
pass-through (e.g., we just take extant annotations and repackage in 
easier to use formats), so the updating is dependent to a certain extent 
on others.

Anyway, there is the mirbase.db package as well as the RmiR.Hs.miRNA 
package. The latter seems more to your liking.

Best,

Jim


> Any guidance would be greatly appreciated.
> Thanks,
> Ranjani
>
>   -- output of sessionInfo():
>
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] VennDiagram_1.6.0  edgeR_3.0.8        limma_3.14.4       DESeq_1.10.1       lattice_0.20-15    locfit_1.5-9.1
> [7] Biobase_2.18.0     BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>   [1] annotate_1.36.0      AnnotationDbi_1.20.7 DBI_0.2-7            genefilter_1.40.0    geneplotter_1.36.0
>   [6] IRanges_1.16.6       parallel_2.15.2      RColorBrewer_1.0-5   RSQLite_0.11.4       splines_2.15.2
> [11] stats4_2.15.2        survival_2.37-4      tools_2.15.2         XML_3.98-1.1         xtable_1.7-1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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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