Hi Abdul, Good that you mention KEGG and I should probably have mentioned the KEGG.db package for step 1 of the proposed workflow. Even though I've no direct experience with it. Unfortunately, my understanding is that it's about to be deprecated (because of licensing issues). I heard there are some alternatives though. Hopefully more knowledgeable people will chime in with helpful suggestions. Cheers, H. On 06/27/2013 09:57 PM, Abdul Rawoof wrote: > 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 at="" fhcrc.org=""> <mailto:hpages at="" fhcrc.org="">> 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 at r-project.org <mailto:bioconductor at="" r-project.org=""> > 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 at fhcrc.org <mailto:hpages at="" fhcrc.org=""> > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > -- 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 at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319