get al microRNA target sites for a given gene
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@javier-perez-florido-3121
Last seen 4.5 years ago
Dear list, How can I obtain all microRNA target sites for a given gene? I've checked other packages such as miRBase, but it provides information in the other way....(input is a microRNA). Thanks, Javier
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@james-w-macdonald-5106
Last seen 11 hours ago
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Hi Javier, On 10/15/2012 11:42 AM, Javier P?rez Florido wrote: > Dear list, > How can I obtain all microRNA target sites for a given gene? Do you want miRNA target *sites* or target genes? Also, what do you mean by 'all'? To my knowledge, miRNA->mRNA mapping is based on sequence similarity, which implies a cutoff that can be varied (so 'all' is a relative term). Anyway, you could use the microCosm files that you can download here: http://www.ebi.ac.uk/enright-srv/microcosm/cgi- bin/targets/v5/download.pl The files contain the Ensembl transcript ID, as well as the chr, start and end. So a simple tapply() (or by()) will give you the by- transcript miRNAs, and you can go from there. Best, Jim > I've checked other packages such as miRBase, but it provides > information in the other way....(input is a microRNA). > > Thanks, > Javier > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi James, Thanks for your reply. What I want is something like this: http://docs.bioinfo.cipf.es/projects/cellbase/wiki/Feature_rest_ws_api Cellbase retrieves all microRNA targets sites for a given gene, for example, for BRCA2 gene: * http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/gene/BRCA2/ mirna_target *I can use this webservice through R, but would like to know if some Bioconductor package can handle this.... Thanks again Javier On 15/10/12 17:53, James W. MacDonald wrote: > Hi Javier, > > On 10/15/2012 11:42 AM, Javier Pérez Florido wrote: >> Dear list, >> How can I obtain all microRNA target sites for a given gene? > > Do you want miRNA target *sites* or target genes? Also, what do you > mean by 'all'? To my knowledge, miRNA->mRNA mapping is based on > sequence similarity, which implies a cutoff that can be varied (so > 'all' is a relative term). > > Anyway, you could use the microCosm files that you can download here: > > http://www.ebi.ac.uk/enright-srv/microcosm/cgi- bin/targets/v5/download.pl > > The files contain the Ensembl transcript ID, as well as the chr, start > and end. So a simple tapply() (or by()) will give you the > by-transcript miRNAs, and you can go from there. > > Best, > > Jim > > >> I've checked other packages such as miRBase, but it provides >> information in the other way....(input is a microRNA). >> >> Thanks, >> Javier >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Hi Javier, On 10/16/2012 3:06 AM, Javier P?rez Florido wrote: > Hi James, > Thanks for your reply. > What I want is something like this: > http://docs.bioinfo.cipf.es/projects/cellbase/wiki/Feature_rest_ws_api > > Cellbase retrieves all microRNA targets sites for a given gene, for > example, for BRCA2 gene: > * > http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/gene/BRCA 2/mirna_target > > > > *I can use this webservice through R, but would like to know if some > Bioconductor package can handle this.... There is the mirbase.db package, but you would need to poke around to see what it can do - I have never found it particularly helpful for my use cases. Best, Jim > Thanks again > Javier > > > On 15/10/12 17:53, James W. MacDonald wrote: >> Hi Javier, >> >> On 10/15/2012 11:42 AM, Javier P?rez Florido wrote: >>> Dear list, >>> How can I obtain all microRNA target sites for a given gene? >> >> Do you want miRNA target *sites* or target genes? Also, what do you >> mean by 'all'? To my knowledge, miRNA->mRNA mapping is based on >> sequence similarity, which implies a cutoff that can be varied (so >> 'all' is a relative term). >> >> Anyway, you could use the microCosm files that you can download here: >> >> http://www.ebi.ac.uk/enright-srv/microcosm/cgi- bin/targets/v5/download.pl >> >> >> The files contain the Ensembl transcript ID, as well as the chr, >> start and end. So a simple tapply() (or by()) will give you the >> by-transcript miRNAs, and you can go from there. >> >> Best, >> >> Jim >> >> >>> I've checked other packages such as miRBase, but it provides >>> information in the other way....(input is a microRNA). >>> >>> Thanks, >>> Javier >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Dear Javier, On 16/10/12 15:03, James W. MacDonald wrote: > Hi Javier, > > On 10/16/2012 3:06 AM, Javier P?rez Florido wrote: >> Hi James, >> Thanks for your reply. >> What I want is something like this: >> http://docs.bioinfo.cipf.es/projects/cellbase/wiki/Feature_rest_ws_api >> >> Cellbase retrieves all microRNA targets sites for a given gene, for >> example, for BRCA2 gene: >> * >> http://ws.bioinfo.cipf.es/cellbase/rest/latest/hsa/feature/gene/BRC A2/mirna_target >> >> >> >> >> *I can use this webservice through R, but would like to know if some >> Bioconductor package can handle this.... > > There is the mirbase.db package, but you would need to poke around to > see what it can do - I have never found it particularly helpful for my > use cases. > > Best, > > Jim > > >> Thanks again >> Javier >> >> >> On 15/10/12 17:53, James W. MacDonald wrote: >>> Hi Javier, >>> >>> On 10/15/2012 11:42 AM, Javier P?rez Florido wrote: >>>> Dear list, >>>> How can I obtain all microRNA target sites for a given gene? >>> >>> Do you want miRNA target *sites* or target genes? Also, what do you >>> mean by 'all'? To my knowledge, miRNA->mRNA mapping is based on >>> sequence similarity, which implies a cutoff that can be varied (so >>> 'all' is a relative term). >>> >>> Anyway, you could use the microCosm files that you can download here: >>> >>> http://www.ebi.ac.uk/enright-srv/microcosm/cgi- bin/targets/v5/download.pl >>> >>> >>> The files contain the Ensembl transcript ID, as well as the chr, >>> start and end. So a simple tapply() (or by()) will give you the >>> by-transcript miRNAs, and you can go from there. >>> >>> Best, >>> >>> Jim >>> >>> >>>> I've checked other packages such as miRBase, but it provides >>>> information in the other way....(input is a microRNA). >>>> >>>> Thanks, >>>> Javier >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > I don't think that a package which aggregates microRNA target site prediction from different resources, such as the one you mentioned (cellbase), is currently available on Bioconductor. The only one that I know of that is a _single_ source of predicted target sites is targetscan which is on Bioconductor for both human and mouse which is updated regularly. So for example from your example with BRCA2: > library("targetscan.Hs.eg.db") > library("org.Hs.eg.db") > get(get("BRCA2", revmap(org.Hs.egSYMBOL)), targetscan.Hs.egTARGETS) Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : value for "675" not found this is because no conserved sites are predicted in the 3' UTR of BRCA2 by targetscan, on the other hand BRCA1 does: > get(get("BRCA1", revmap(org.Hs.egSYMBOL)), targetscan.Hs.egTARGETS) [1] "miR-132/212/212-3p" "miR-132/212/212-3p" "miR-132/212/212-3p" [4] "miR-132/212/212-3p" "miR-132/212/212-3p" "miR-7/7ab" [7] "miR-7/7ab" "miR-7/7ab" "miR-7/7ab" [10] "miR-7/7ab" "miR-205/205ab" "miR-205/205ab" [13] "miR-205/205ab" "miR-205/205ab" "miR-205/205ab" [16] "miR-218/218a" "miR-218/218a" "miR-218/218a" [19] "miR-218/218a" "miR-218/218a" "miR-125a-3p/1554" [22] "miR-125a-3p/1554" "miR-125a-3p/1554" "miR-125a-3p/1554" [25] "miR-125a-3p/1554" notice the repetitions indicating multiple target sites within the UTR. HTH, J.
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