get al microRNA target sites for a given gene
1
0
Entering edit mode
@javier-perez-florido-3121
Last seen 6.6 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
microRNA microRNA • 2.0k views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States
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
ADD COMMENT
0
Entering edit mode
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]]
ADD REPLY
0
Entering edit mode
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
ADD REPLY
0
Entering edit mode
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.
ADD REPLY

Login before adding your answer.

Traffic: 620 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6