Thank you very much.
Now I have to push my inquiry a little bit further ... sorry for being pedantic. 
Do you know, or can you help me finf out, the correspondence naming convention between the BioMart databases and miRecords and TarBase ? 
Thanks to your help I learnt how to find the association between miRNA and gene-3UTR region. For instance:

Similarity	hsa-miR-130a	miRanda	miRNA_target	2	120825363	120825385	+	.	16.5359	1.687830e-02	ENST00000295228	INHBB

miRNA identifier is        "hsa-miR-130a"
Feature is:                       "miRNA_target"
Chromosome is:           2
Start is:                            120825363
End is:                             120825385	
TRANSCRIPT_ID is:     ENST00000295228
EXTERNAL_NAME is:   INHBB

I downloaded the VALIDATED Targets from miRecords and saved it as an XLS file. 
I browsed such XLS file looking for the above miRNA identifier "hsa-miR-130a" and found  the following 4 records
where the target gene names (not unique) are respectively:  "MCSF","MAFB","GAX","HOXA5", 
the Target gene_Refseq_acc are the NM.... strings, 
the Target site_number is known and equal to 2 only for the first two records 

14697198	Homo sapiens	human	MCSF	NM_000757.3	2	Homo sapiens	hsa-miR-130a
14697198	Homo sapiens	human	MCSF	NM_000757.3	2	Homo sapiens	hsa-miR-130a
16549775	Homo sapiens	human	MAFB	NM_005461.3		Homo sapiens	hsa-miR-130a
17957028	Homo sapiens	human	GAX	        NM_005924.4		Homo sapiens	hsa-miR-130a
17957028	Homo sapiens	human	GAX	        NM_005924.4		Homo sapiens	hsa-miR-130a
17957028	Homo sapiens	human	GAX	        NM_005924.4		Homo sapiens	hsa-miR-130a
17957028	Homo sapiens	human	HOXA5	NM_019102.2		Homo sapiens	hsa-miR-130a

It looks like miRNAs naming convebtion is the same for BioMart and miRecords databases 
My problem is the apparently different genes naming convention.
How can I map  the gene identifier used in BioMart databases  to the gene identifiers used in miRecords ?
Without such *hopefully* 1-1 mapping function I cannot use the information across databases.
On the other hand, I cannot see how to get the 3UTR region sequences from miRecords only.

Any suggestion and/or comment is more than welcome.
 Thank you in advance for your attention.
Maura

-----Messaggio originale-----
Da: michael watson (IAH-C) [mailto:michael.watson@bbsrc.ac.uk]
Inviato: gio 25/06/2009 8.39
A: mauede@alice.it; Sean Davis
Cc: bioconductor@stat.math.ethz.ch
Oggetto: RE: [BioC] how to find the VALIDATED pair (miRNA, gene-3'UTR-sequence)
 
They are predicted.
 
The only databases of experimentally predicted taregst are TarBase and miRecords, and when I last looked they had 1300 and 1135 records respectively.
 
Mick 

________________________________

From: bioconductor-bounces@stat.math.ethz.ch on behalf of mauede@alice.it
Sent: Thu 25/06/2009 4:57 AM
To: Sean Davis
Cc: bioconductor@stat.math.ethz.ch
Subject: [BioC] how to find the VALIDATED pair (miRNA, gene-3'UTR-sequence)



Thank you very much.
I believe I can use biomaRt functions to get the 3'UTR sequences through providing the crhomosome name and start/end sequence coordinates.
However I am not sure that the text file I downloaded from http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl
that is "arch.v5.txt.homo_sapiens" contains (points to) the VALIDATED miRNA <-> gene-3'UTR sequences (or coordinates of them).
Since the prediction code "miRANDA" is mentioned, my question is: 
are the (miRNA, gene-3'UTR-sequence) pairs listed in the files downloadable from   http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl 
experimentally VALIDATED or computationally PREDICTED ?
At he time being I definitely need the (miRNA,gene-3'UTR-sequences) experimentally VALIDATED pairs.
Please, correct me if I am mistaken .
Thank you so much,
Maura

-----Messaggio originale-----
Da: Sean Davis [mailto:seandavi@gmail.com]
Inviato: mer 24/06/2009 18.28
A: mauede@alice.it
Cc: bioconductor@stat.math.ethz.ch
Oggetto: Re: [BioC] how to find the validated pair (miRNA, gene-3'UTR-sequence)

On Wed, Jun 24, 2009 at 11:45 AM, <mauede@alice.it> wrote:

> Sorry for my misuse of Biology nomenclature. I am still very confused.
>
> My first task (very trivial for you) is to generate a text files containing
> a list of Homo-Sapiens validated miRNAs (microRNA-identifier, sequence)
> and relative 3'UTR regions (gene-identifier, 3'UTR-sequence).


Hi, Maura.  See here:

http://microrna.sanger.ac.uk/cgi-bin/targets/v5/download.pl

If you download the text file for human, it looks like:

Similarity      hsa-miR-647     miRanda miRNA_target    2
120824263       120824281       +       .       16.3205 3.701400e-06
ENST00000295228 INHBB
Similarity      hsa-miR-130a    miRanda miRNA_target    2
120825363       120825385       +       .       16.5359 1.687830e-02
ENST00000295228 INHBB

>From here, you have the miR name, the chromosome (2 in this case), the
chromosome start and end positions, and the strand.  You can use this to get
the sequence from the genome (the fasta sequence for those locations).  The
transcript name (ENST....) is from the Ensembl database, so there is plenty
of information via biomaRt, if necessary, but the HUGO gene symbol is given
in the last column.

Several of the code snippets you give below give similar information.  If
you are concerned about what a specific data source is giving you, you
should probably contact that data source directly via email.  Most websites
offer a "contact us" link.

If this isn't what you need, then perhaps you can show more specifically how
this information is not meeting your needs.  Know that you may have to do a
little bit of programming to get things into exactly the formats that you
like.

Sean


>
> I realize this is just a matter of retrieving all known information. The
> difficulty for me is where to find the pair (miRNA, gene-3'UTR) matching
> information.
> In the following I downloaded a lot of stuff but I do not know how to put
> the pieces together to fulfill my task.
> I think the 3'UTR sequences can be retrieved through function "getSequence"
> from package "biomaRt"m .... if only I knew which parameters to pass to such
> a function to achieve my goal.
>
> 1) Function "hsSeqs" from package "microRNA" produces 677 miRNAs entries
> ex.  hsa-let-7a   "UGAGGUAGUAGGUUGUAUAGUU"
>  Are such miRNAs validated ?
>  If the answer is "yes" then how can I retrieve the correspondent
> gene-3'UTR regions ?
>
> 2) Function "hsSeqs" from package "microRNA" produces a matrix 709015x 6
> contaiing miRNA identifiers
>   and apparently some data from the paired gene.
> ex.      name             target            chrom start       end
> strand
>   [1,] "hsa-miR-647"    "ENST00000295228" "2"   "120824263" "120824281" "+"
>   [2,] "hsa-miR-130a"   "ENST00000295228" "2"   "120825363" "120825385" "+"
>
>
>  Again. how can I retrieve the correspondent gene-3'UTR regions from the
> above data ?


Note my answer above.  The gene 3'UTR information is there, but you may need
to do some calculations, depending on what you want.  Also, note that
"genes" do not have 3'UTRs--only transcripts have that.


>
>
> 3)  Function "s3utr" from package "microRNA" produces 112  3'UTR entries
> ex.
> "CCTGCCCGCCCGCATGGCCAGCCAGTGGCAAGCTGCCGCCCCCACTCTCCGGGCACCGTCTCCTGCCTGTGCGTCCGCCC
>
> ACCGCTGCCCTGTCTGTTGCGACACCCTCCCCCCCACATACACACGCAGCGTTTTGATAAATTATTGGTTTTCAACG"
>
>   Where do such 3'UTR come from ? Which (miRNA, gene) do they belong to ?
>
> 4) I downloaded the file "mature.fa"  (Fasta format sequences of all mature
> miRNA sequences) from http://microrna.sanger.ac.uk/sequences/ftp.shtml
>    The file contais a number of records starting withthe miRNA identifier.
> ex:  hsa-miR-943        miRanda miRNA_target    9885484 9885504 15.6748
> 4.721740e-02    +       .       URL "
> http://www.ensembl.org/homo_sapiens/geneview?gene=ENST00000302092"
> hsa-miR-944     miRanda miRNA_target    9885188 9885209 16.602
>  1.659470e-03    +       .       URL "
> http://www.ensembl.org/homo_sapiens/geneview?gene=ENST00000302092"
>
>  Where are the 3'UTR regions indicated in the above records ?
>
>
> 5) I downloaded miRNA Validated Targets from
> http://mirecords.umn.edu/miRecords/download.php.
>    It generated a huge XLS file with alot of data.
> ex:   Pubmed_id Target gene_species_scientific  Target gene_species_common
>      Target gene_name        Target gene_Refseq_acc  Target site_number
>  miRNA_species   miRNA_mature_ID miRNA_regulation        Reporter_target
> gene/region     Reporter link element   Test_method_inter       Target gene
> mRNA_level  Original description    Mutation_target region  Post
> mutation_method    Original description_mutation_region    Target
> site_position    A       Reporter_target site    Reporter link element
> Test_method_inter_site  Original description_inter_site Mutation_target site
>    Post mutation_method_site       Original description_mutation_site
>  Mutiple site mutation note      Additional note
> 12808467        Homo sapiens    human   Hes1    NM_198155.2     1
> Homo sapiens    hsa-miR-23a     mutation                        Western
> blotting                Next, to examine whether expression of the gene for
> Hes1 is regulated by miR-23, we introduced synthetic miR-23 or mutant miR-23
> (Fig. 2a) into undifferentiated NT2 cells. When synthetic miR-23 was
> introduced at 2 mMinto undifferentiated NT2 cells,the intracellular level of
> Hes1 fell significantly (Fig. 2b).By contrast,in the presence of synthetic
> mutant miR-23,the level of Hes1 in undifferentiated NT2 cells remained
> unchanged and similar to that in untreated wild-type NT2 cells (Fig. 2b).
>                        801     overexpression by mature miRNA transfection
>   luciferase      target site(five copies of the target sequence) activity
> assay  Furthermore, the luciferase activity of LucSTS23 in undifferentiated
> NT2 cells that had been treated with synthetic miR-23 was lower than that in
> untreated wild-type NT2 cells (Fig. 3c).      Yes     Luciferase activity
> assay       Furthermore, the luciferase activity of LucSTS23 in
> undifferentiated NT2 cells that had been treated with synthetic miR-23 was
> lower than that in untreated wild-type NT2 cells (Fig. 3c).
>
> Thank you in advance for helping me out of my misery.
> Maura
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tutti i telefonini TIM!


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