28 Jun 2013 06:57
Re: Regarding extraction of 3' and 5'UTRs and exonic region of a gene.
Abdul Rawoof <abdul87.edu@...>
2013-06-28 04:57:30 GMT
2013-06-28 04:57:30 GMT
Thanks for your kind suggestion and I will try to follow your suggested workflow and obviously it will take time to learn all this packages as I never go through it. One more thing I want to ask that how can I download the list of all available cancer genes for human from Kegg database for wnt signaling pathways?? Please forgive me if I asked any senseless question as I have not tried that mentioned packages till now. Thanks, Abdul Rawoof On Thu, Jun 27, 2013 at 11:01 PM, Hervé Pagès <hpages@...> wrote: > Hi Abdul, > > Suggested workflow: > > 1. Build the list of genes involved in the particular cancer you're > interested in. Could be a vector of gene ids or transcript ids (not > all transcripts are necessarily linked to a gene). > > Suggested tools (no exhaustive): GO.db and org.Hs.eg.db packages, > maybe the DO.db package, etc... I'm not sure what would be the best > tool for this. But maybe you already have your list of genes? > > 2. Use the TxDb.Hsapiens.UCSC.hg19.**knownGene + GenomicFeatures packages > to extract the coordinates of the 5'UTRs and 3'UTRs. > Use the fiveUTRsByTranscript() and threeUTRsByTranscript() functions > for this. They'll return the result in a GRangesList object (you'll > have to become a bit familiar with those objects first). > > 3. Use the BSgenome.Hsapiens.UCSC.hg19 package and the > extractTranscriptsFromGenome() function from the GenomicFeatures > package to extract the UTR sequences. > The name of the function is misleading but it can be used to extract > CDS or UTR sequences in addition to transcript sequences. > > If you've never used those tools before, it will take you some time to > get familiarized with them. Your best friends are the man pages for the > individual functions/classes you're going to run into (don't miss the > examples section) and the vignettes in the GenomicRanges and > GenomicFeatures package. > > Let us know if you have specific questions or run into specific problems > (show us what you've done and explain the problem -- don't forget your > sessionInfo()). > > Good luck, > H. > > > On 06/27/2013 01:58 AM, Abdul Rawoof wrote: > >> Hello everyone, >> >> >> Could anyone show me the way how can I extract the *3' and 5' UTRs and >> exonic regions *of all *Human genes* from *Ensembl and Kegg database* that >> are involved in particular cancer specially *breast cancer *using >> >> R/Biocondutor. >> >> Thanks in advance. >> >> Abdul Rawoof >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@... >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.ch/mailman/listinfo/bioconductor> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor> >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@... > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]
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