If I got it right dataset  "hsSeqs" (from microRNA package) has the same content as file "mature.fa" that can be downloaded from MirBase  for Homo Sapiens miRNA identifiers and sequences.  Whereas dataset  "hsTargets" contains all  target genes for Homo Sapiens miRNAs listed in  file "mature.fa"  but also for those listed in file  "maturestar.fa" ???

My purpose is to gather all Homo Sapiens validated miRNAs together with their relative target genes 3UTR sequences, 
Therefore, if I am guessing right, I can as well use Homo Sapiens  subset of files "mature.fa" and "maturestar.fa" and work this out  together with dataset "hsTargets" and on-line bioMart for the transcripts sequence. Am I right ?

Thank you so much.
Maura



-----Messaggio originale-----
Da: Peter Robinson [mailto:peter.robinson@charite.de]
Inviato: lun 19/10/2009 14.42
A: mauede@alice.it
Cc: cwon2@fhcrc.org; Bioconductor List
Oggetto: Re: [BioC] difference between  "hsa-miR-xxx" and  "hsa-miR-xxx*"
 
mauede@alice.it wrote:
> I'd like to figure out the difference between validated miRNAs whose identifiers only differ by a "*".

See the following from miRbase 
(http://www.mirbase.org/help/nomenclature.shtml):

When the relative abundancies clearly indicate which is the 
predominantly expressed miRNA, the mature sequences are assigned names 
of the form miR-56 (the predominant product) and miR-56* (from the 
opposite arm of the precursor).


Note that the targets of the *-version are generally different from that 
of the predominant product.

-Peter



> 
> I downloaded the miRNA  datasets "hsSeqs" and "hsTargets" and noticed  that none of the miRNA identifiers
>  in dataset "hsSeqs" contains the character "*"  whereas many miRNA identifiers in dataset  "hsTargets" end with
>  the character "*". I checked a couple of them and found out that the set of Ensembl-Transcript_Identifiers for 
> "hsa-miR-18a" and the set of Ensembl-Transcript_Identifiers for "hsa-miR-18a*" are disjoined.
> Therefore "hsa-miR-18a"  and  "hsa-miR-18a*" seem to be two different entities. I wonder whether 
>   "hsa-miR-18a"  and  "hsa-miR-18a*" share the same sequence even if apparently they bind to different
> gene transcripts.  
> 
> My naive question is: 
> how can I find the sequence of those miRNAs whose identifier ends with a "*" given that none of the miRNA identifiers in dataset "hsSeqs" contain a "*" ?
> In short, I kind of realized that  "hsa-miR-xxx*"  is an evolution of  "hsa-miR-xxx". 
> But when  it comes to dig out the 3UTR sequences of the relative targets which one of the two versions ( "hsa-miR-xxx"  or  "hsa-miR-xxx*" ) shall I ascribe them to ?
> 
> Thank you in advance for your attention.
> Maura 
> 
> 
> 
> tutti i telefonini TIM!
> 
> 
> 
> 
> 
> tutti i telefonini TIM!
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-- 
Dr. med. Peter N. Robinson, MSc.
Institut für Medizinische Genetik
Universitätsklinikum Charite
Humboldt-Universität
Augustenburger Platz 1
13353 Berlin
Germany
voice: 49-30-450569124
fax:   49-30-450569915
email: peter.robinson@charite.de
http://compbio.charite.de/
http://www.human-phenotype-ontology.org




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