Question

RefSeq summary from biomaRt

0

Entering edit mode

Gad Abraham ▴ 110

@gad-abraham-2948

Last seen 10.3 years ago

Hi, Is it possible to get RefSeq summaries for a given gene using biomaRt (or any other tool?) From ensembl I can only get RefSeq DNA ID, RefSeq Predicted DNA ID, RefSeq Protein ID, RefSeq Predicted Protein ID. Specifically, I'm looking for mentions of alternative splicing (e.g., "Alternatively spliced transcript variants encoding different isoforms have been described"). Thanks, Gad -- Gad Abraham MEng Student, Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabraham at csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham

• 2.1k views

ADD COMMENT • link updated 15.5 years ago by Steve Lianoglou ★ 13k • written 15.5 years ago by Gad Abraham ▴ 110

score 0 · Answer 1 · 2009-06-25

0

Entering edit mode

Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 22 months ago

United States

Hi, On Jun 25, 2009, at 11:43 PM, Gad Abraham wrote: > Hi, > > Is it possible to get RefSeq summaries for a given gene using > biomaRt (or any other tool?) From ensembl I can only get RefSeq DNA > ID, RefSeq Predicted DNA ID, RefSeq Protein ID, RefSeq Predicted > Protein ID. > > Specifically, I'm looking for mentions of alternative splicing > (e.g., "Alternatively spliced transcript variants encoding different > isoforms have been described"). Would the presence of multiple ensembl_transcript_id's for one gene give you the information you need? For example: R> getBM(attributes=c('hgnc_symbol', 'ensembl_transcript_id', 'refseq_dna', 'transcript_start', 'transcript_end'), filters='hgnc_symbol', value='AKNA', mart=hmart) hgnc_symbol ensembl_transcript_id refseq_dna transcript_start transcript_end 1 AKNA ENST00000223791 116138266 116179065 2 AKNA ENST00000320310 116136257 116162197 3 AKNA ENST00000374074 116138266 116179736 4 AKNA ENST00000312033 116161188 116190182 5 AKNA ENST00000394574 116178067 116196506 6 AKNA ENST00000374075 116136257 116196506 7 AKNA ENST00000394582 116136257 116190037 8 AKNA ENST00000374088 NM_030767 116138228 116190064 9 AKNA ENST00000307564 116136257 116196506 10 AKNA ENST00000374079 116136257 116196506 -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos

ADD COMMENT • link 15.5 years ago Steve Lianoglou ★ 13k

0

Entering edit mode

On 26/6/09 2:15 PM, Steve Lianoglou wrote: > Hi, > > On Jun 25, 2009, at 11:43 PM, Gad Abraham wrote: > >> Hi, >> >> Is it possible to get RefSeq summaries for a given gene using biomaRt >> (or any other tool?) From ensembl I can only get RefSeq DNA ID, RefSeq >> Predicted DNA ID, RefSeq Protein ID, RefSeq Predicted Protein ID. >> >> Specifically, I'm looking for mentions of alternative splicing (e.g., >> "Alternatively spliced transcript variants encoding different isoforms >> have been described"). > > > Would the presence of multiple ensembl_transcript_id's for one gene give > you the information you need? > > For example: > > R> getBM(attributes=c('hgnc_symbol', 'ensembl_transcript_id', > 'refseq_dna', 'transcript_start', 'transcript_end'), > filters='hgnc_symbol', value='AKNA', mart=hmart) > hgnc_symbol ensembl_transcript_id refseq_dna transcript_start > transcript_end > 1 AKNA ENST00000223791 116138266 116179065 > 2 AKNA ENST00000320310 116136257 116162197 > 3 AKNA ENST00000374074 116138266 116179736 > 4 AKNA ENST00000312033 116161188 116190182 > 5 AKNA ENST00000394574 116178067 116196506 > 6 AKNA ENST00000374075 116136257 116196506 > 7 AKNA ENST00000394582 116136257 116190037 > 8 AKNA ENST00000374088 NM_030767 116138228 116190064 > 9 AKNA ENST00000307564 116136257 116196506 > 10 AKNA ENST00000374079 116136257 116196506 Thanks Steve, As far as I understand, having multiple splice variants doesn't in itself necessarily indicate that alternative splicing is important for the gene's function. My plan was to find such genes through the RefSeq description, and then if there is known alternative splicing, get the variants. Gad -- Gad Abraham MEng Student, Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabraham at csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham

ADD REPLY • link 15.5 years ago Gad Abraham ▴ 110

0

Entering edit mode

On Fri, Jun 26, 2009 at 3:53 AM, Gad Abraham <gabraham@csse.unimelb.edu.au>wrote: > On 26/6/09 2:15 PM, Steve Lianoglou wrote: > >> Hi, >> >> On Jun 25, 2009, at 11:43 PM, Gad Abraham wrote: >> >> Hi, >>> >>> Is it possible to get RefSeq summaries for a given gene using biomaRt >>> (or any other tool?) From ensembl I can only get RefSeq DNA ID, RefSeq >>> Predicted DNA ID, RefSeq Protein ID, RefSeq Predicted Protein ID. >>> >>> Specifically, I'm looking for mentions of alternative splicing (e.g., >>> "Alternatively spliced transcript variants encoding different isoforms >>> have been described"). >>> >> >> >> Would the presence of multiple ensembl_transcript_id's for one gene give >> you the information you need? >> >> For example: >> >> R> getBM(attributes=c('hgnc_symbol', 'ensembl_transcript_id', >> 'refseq_dna', 'transcript_start', 'transcript_end'), >> filters='hgnc_symbol', value='AKNA', mart=hmart) >> hgnc_symbol ensembl_transcript_id refseq_dna transcript_start >> transcript_end >> 1 AKNA ENST00000223791 116138266 116179065 >> 2 AKNA ENST00000320310 116136257 116162197 >> 3 AKNA ENST00000374074 116138266 116179736 >> 4 AKNA ENST00000312033 116161188 116190182 >> 5 AKNA ENST00000394574 116178067 116196506 >> 6 AKNA ENST00000374075 116136257 116196506 >> 7 AKNA ENST00000394582 116136257 116190037 >> 8 AKNA ENST00000374088 NM_030767 116138228 116190064 >> 9 AKNA ENST00000307564 116136257 116196506 >> 10 AKNA ENST00000374079 116136257 116196506 >> > > Thanks Steve, > > As far as I understand, having multiple splice variants doesn't in itself > necessarily indicate that alternative splicing is important for the gene's > function. My plan was to find such genes through the RefSeq description, and > then if there is known alternative splicing, get the variants. Hi, Gad. I'm not sure what your goal is for looking for such genes, but I think it likely that nearly all genes undergo alternative splicing under the right conditions, so any gene that has multiple transcripts in a database like RefSeq (or Ensembl) is likely to be a viable candidate. See here for details, as an example. http://www.nature.com/nature/journal/v456/n7221/full/nature07509.html Hope that helps. Sean [[alternative HTML version deleted]]

ADD REPLY • link 15.5 years ago Sean Davis 21k