R: R: how to find the VALIDATED pair (miRNA, gene-3'UTR-sequence)

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mauede@alice.it ▴ 870

@mauedealiceit-3511

Last seen 10.2 years ago

Thank you very much. Where can I get a glossary of the nomenclature used to query such data bases ? As a physicist I have no idea what the values of attributes and filters .... mean. Maura -----Messaggio originale----- Da: Steve Lianoglou [mailto:mailinglist.honeypot@gmail.com] Inviato: gio 25/06/2009 16.02 A: mauede@alice.it Cc: bioconductor List Oggetto: Re: [BioC] R: how to find the VALIDATED pair (miRNA, gene-3 'UTR-sequence) One more thing to add: >> Similarity hsa-miR-130a miRanda miRNA_target 2 120825363 120825385 >> + . 16.5359 1.687830e-02 ENST00000295228 INHBB > R> library(biomaRt) > R> hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl') > R> refseqs <- > c > ("NM_000757 > ","NM_000757 > ","NM_005461","NM_005924","NM_005924","NM_005924","NM_019102") > R> gene.map <- getBM(attributes=c('hgnc_symbol', 'ensembl_gene_id', > 'ensembl_transcript_id','refseq_dna'), filters='refseq_dna', > value=refseqs, mart=hmart) > > R> gene.map > hgnc_symbol ensembl_gene_id ensembl_transcript_id refseq_dna > 1 CSF1 ENSG00000184371 ENST00000369802 NM_000757 > 2 MAFB ENSG00000204103 ENST00000396967 NM_005461 > 3 MEOX2 ENSG00000106511 ENST00000262041 NM_005924 > 4 HOXA5 ENSG00000106004 ENST00000222726 NM_019102 Your original ensembl transcript wasn't included in our result, so instead of telling the `getBM` function to use a list of refseq IDs to get info for, we can flip this around and find out what refseq ID your "ENST00000295228" transcript points to. Using the same `hmart` object, you can do it like so: R> getBM(attributes=c('hgnc_symbol', 'ensembl_gene_id', 'ensembl_transcript_id','refseq_dna'), filters='ensembl_transcript_id', value='ENST00000295228', mart=hmart) hgnc_symbol ensembl_gene_id ensembl_transcript_id refseq_dna 1 INHBB ENSG00000163083 ENST00000295228 NM_002193 Note we just had to change the type of ID we are passing to the `filters` parameter. -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact tutti i telefonini TIM! [[alternative HTML version deleted]]

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ADD COMMENT • link 15.4 years ago mauede@alice.it ▴ 870

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 21 months ago

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> Thank you very much. > Where can I get a glossary of the nomenclature used to query such > data bases ? > As a physicist I have no idea what the values of attributes and > filters .... mean. > I'm not sure that there's one place you can go that will give you the full description of what each attribute means. That having been said, you can get a list of names you can use as attributes/filters by using the `listAttributes` function, which will give you a data frame (~ 665 rows for humans) that give you an attribute to "human readable" map: R> library(biomaRt) R> hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl') R> head(listAttributes(hmart)) name description 1 ensembl_gene_id Ensembl Gene ID 2 ensembl_transcript_id Ensembl Transcript ID 3 ensembl_peptide_id Ensembl Protein ID 4 canonical_transcript_stable_id Canonical transcript stable ID(s) 5 description Description 6 chromosome_name Chromosome Name ... If you need more info than what's provided in the "description" column, you''ll have to do some hunting, or just ask on the list if you're getting stuck. HTH, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos

ADD COMMENT • link 15.4 years ago Steve Lianoglou ★ 13k

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mauede@alice.it ▴ 870

@mauedealiceit-3511

Last seen 10.2 years ago

What is the attribute correspondent to the miR name (ex. "hsa-miR- 130a") ? I have to link the gene information (actually right now I am only intrested to the 3'UTR sequence) to the miRNA for which the gene in question is a target. Thak you. Maura -----Messaggio originale----- Da: Steve Lianoglou [mailto:mailinglist.honeypot@gmail.com] Inviato: gio 25/06/2009 16.02 A: mauede@alice.it Cc: bioconductor List Oggetto: Re: [BioC] R: how to find the VALIDATED pair (miRNA, gene-3 'UTR-sequence) One more thing to add: >> Similarity hsa-miR-130a miRanda miRNA_target 2 120825363 120825385 >> + . 16.5359 1.687830e-02 ENST00000295228 INHBB > R> library(biomaRt) > R> hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl') > R> refseqs <- > c > ("NM_000757 > ","NM_000757 > ","NM_005461","NM_005924","NM_005924","NM_005924","NM_019102") > R> gene.map <- getBM(attributes=c('hgnc_symbol', 'ensembl_gene_id', > 'ensembl_transcript_id','refseq_dna'), filters='refseq_dna', > value=refseqs, mart=hmart) > > R> gene.map > hgnc_symbol ensembl_gene_id ensembl_transcript_id refseq_dna > 1 CSF1 ENSG00000184371 ENST00000369802 NM_000757 > 2 MAFB ENSG00000204103 ENST00000396967 NM_005461 > 3 MEOX2 ENSG00000106511 ENST00000262041 NM_005924 > 4 HOXA5 ENSG00000106004 ENST00000222726 NM_019102 Your original ensembl transcript wasn't included in our result, so instead of telling the `getBM` function to use a list of refseq IDs to get info for, we can flip this around and find out what refseq ID your "ENST00000295228" transcript points to. Using the same `hmart` object, you can do it like so: R> getBM(attributes=c('hgnc_symbol', 'ensembl_gene_id', 'ensembl_transcript_id','refseq_dna'), filters='ensembl_transcript_id', value='ENST00000295228', mart=hmart) hgnc_symbol ensembl_gene_id ensembl_transcript_id refseq_dna 1 INHBB ENSG00000163083 ENST00000295228 NM_002193 Note we just had to change the type of ID we are passing to the `filters` parameter. -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact tutti i telefonini TIM! [[alternative HTML version deleted]]

ADD COMMENT • link 15.4 years ago mauede@alice.it ▴ 870

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On Sat, Jun 27, 2009 at 1:42 AM, <mauede@alice.it> wrote: > What is the attribute correspondent to the miR name (ex. "hsa-miR- 130a") ? Hi, Maura. This information does not exist directly via biomaRt. You can use the listAttributes() function to see what attributes are available if you are ever in doubt. > > > I have to link the gene information (actually right now I am only intrested > to the 3'UTR sequence) to the miRNA for which the gene in question is a > target. This question has been answered several times for you. You'll want to try those suggestions. At the bottom of emails to this list, you will find a link to search the archives in case you didn't save the emails sent to you earlier. Sean > > -----Messaggio originale----- > Da: Steve Lianoglou [mailto:mailinglist.honeypot@gmail.com] > Inviato: gio 25/06/2009 16.02 > A: mauede@alice.it > Cc: bioconductor List > Oggetto: Re: [BioC] R: how to find the VALIDATED pair (miRNA, > gene-3'UTR-sequence) > > One more thing to add: > > >> Similarity hsa-miR-130a miRanda miRNA_target 2 120825363 > 120825385 > >> + . 16.5359 1.687830e-02 ENST00000295228 INHBB > > > R> library(biomaRt) > > R> hmart <- useMart('ensembl', dataset='hsapiens_gene_ensembl') > > R> refseqs <- > > c > > ("NM_000757 > > ","NM_000757 > > ","NM_005461","NM_005924","NM_005924","NM_005924","NM_019102") > > R> gene.map <- getBM(attributes=c('hgnc_symbol', 'ensembl_gene_id', > > 'ensembl_transcript_id','refseq_dna'), filters='refseq_dna', > > value=refseqs, mart=hmart) > > > > R> gene.map > > hgnc_symbol ensembl_gene_id ensembl_transcript_id refseq_dna > > 1 CSF1 ENSG00000184371 ENST00000369802 NM_000757 > > 2 MAFB ENSG00000204103 ENST00000396967 NM_005461 > > 3 MEOX2 ENSG00000106511 ENST00000262041 NM_005924 > > 4 HOXA5 ENSG00000106004 ENST00000222726 NM_019102 > > > Your original ensembl transcript wasn't included in our result, so > instead of telling the `getBM` function to use a list of refseq IDs to > get info for, we can flip this around and find out what refseq ID your > "ENST00000295228" transcript points to. Using the same `hmart` object, > you can do it like so: > > R> getBM(attributes=c('hgnc_symbol', 'ensembl_gene_id', > 'ensembl_transcript_id','refseq_dna'), > filters='ensembl_transcript_id', value='ENST00000295228', mart=hmart) > > hgnc_symbol ensembl_gene_id ensembl_transcript_id refseq_dna > 1 INHBB ENSG00000163083 ENST00000295228 NM_002193 > > Note we just had to change the type of ID we are passing to the > `filters` parameter. > > -steve > > -- > Steve Lianoglou > Graduate Student: Physiology, Biophysics and Systems Biology > Weill Medical College of Cornell University > > Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.mskc="" c.org="" %7elianos="" contact=""> > > > > > > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > 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 • link 15.4 years ago Sean Davis 21k

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