Hello Rahul, You may read more about knownCanonical transcripts by viewing the UCSC Genes track description page. One way to navigate to this page is by clicking on the "UCSC Genes" link under the Genes and Gene Prediction Tracks group. On the description page (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=knownGene), note: "knownCanonical identifies the canonical isoform of each cluster ID, or gene. Generally, this is the longest isoform."
We don't have tables that show the "most important" transcript. However, if you want to treat isoforms that have RefSeq identifiers preferentially, you could use the kgXref table. kgXref.mRNA contains the identifier (starting with NM_ or NR_) of the transcript that each UCSC Gene was based on. I hope this information is useful and answers your question. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 5/17/2012 3:13 AM, Dr.Rahul Nahar wrote: > Hi > > I had a question regarding the knownCanonical transcripts which we can find > from the UCSC table browser. > Are these the transcripts with all the coding exons of the gene or the > transcript with the longest CDS based on experimental evidence ? > > I assume it to be the latter as not all genes have a canonical transcript ID > associated with them. > > Also how should one choose a single transcript for a gene for annotation > purposes as Canonical transcript might not be the most important / most > studied / most expressed transcript ? For example many publications use the > NM_001203247 transcript for annotating EZH2 mutations (like Y641F) while > according to Canonical transcript (and Cosmic which probably uses Canonical > transcrpt) it should be NM_004456 (and thus the mutation should be Y646F as > in Cosmic) > > Could you please clarify my doubts. > > Thanks& Regards > -- > Rahul > > > > ________________________________ > This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely > for the use of the addressee(s). If you are not the intended recipient, > please notify the sender by e-mail and delete the original message. Further, > you are not to copy, disclose, or distribute this e-mail or its contents to > any other person and any such actions that are unlawful. This e-mail may > contain viruses. Ocimum Biosolutions has taken every reasonable precaution to > minimize this risk, but is not liable for any damage you may sustain as a > result of any virus in this e-mail. You should carry out your own virus > checks before opening the e-mail or attachment. > > > The information contained in this email and any attachments is confidential > and may be subject to copyright or other intellectual property protection. If > you are not the intended recipient, you are not authorized to use or disclose > this information, and we request that you notify us by reply mail or > telephone and delete the original message from your mail system. > > OCIMUMBIO SOLUTIONS (P) LTD > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
