Hello Guy, I don't have a good answer for you on whether or not you have missed any significant references, but one of our engineers suggests that, since there is a limited number of RefSeq mRNAs for chimp, you might consider using the Ensembl Genes track for your comparison instead.
-- Brooke Rhead UCSC Genome Bioinformatics Work Tillinghast, Guy, M.D. wrote on 10/12/10 7:12 AM: > Dear Mary, > > Thanks for your reply. I am interested in compiling a list of proteomic > differences between humans and chimpanzees. I had the impression this > work had been done before, yet a pubmed search only revealed comparisons > regarding the kinome (Anamika et al, 2008), and proteases (Quesada et > al, 2008). > > Have I missed any references? > > To obtain my list, it appears that I will need to browse the chimpanzee > genome at the nucleotide level, using human mRNAs as queries. I can do > this using Bioconductor. Would anyone at UCSC be potentially interested > in checking my list? Presumably, this effort would result in a > publication, for which I would be glad to have co-authors. > > Guy > > -----Original Message----- > From: Mary Goldman [mailto:[email protected]] > Sent: Monday, October 11, 2010 8:25 PM > To: Tillinghast, Guy, M.D. > Cc: [email protected] > Subject: Re: [Genome] The Chimpanzee Proteome. > > Hi Guy, > > The chimpanzee genome is fully sequenced (read the description here: > http://genome.ucsc.edu/cgi-bin/hgGateway?org=Chimp&db=panTro2), however > it has not been as intensively annotated as the human genome. Thus, the > human genome has more mRNAs and protein sequences. > > I hope this information is helpful. Please feel free to contact the > mail list again if you require further assistance. > > Best, > Mary > ------------------ > Mary Goldman > UCSC Bioinformatics Group > > On 10/11/10 5:49 AM, Tillinghast, Guy, M.D. wrote: >> When I download the complete human proteome from the UCSC browser, I >> obtain 28998 entries. >> However, when I employ the same general approach to the Chimpanzee >> proteome, I obtain only 786 entries. Why this discrepancy? >> >> assembly: Mar. 2006 (CGSC2.1/panTro2) >> track: RefSeq Genes >> location: genome >> >> Has the chimpanzee genome not been fully sequenced? >> >> Guy Tillinghast, Newport New, Virginia. >> >> >> CONFIDENTIALITY NOTICE: This e-mail message, including any > attachments, is for the sole use of the intended recipient(s) and may > contain confidential and privileged information. Any unauthorized > review, use, disclosure or distribution is prohibited. If you are not > the intended recipient, please contact the sender by reply e-mail and > destroy all copies of the original message. >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > > > CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is > for the sole use of the intended recipient(s) and may contain confidential > and privileged information. Any unauthorized review, use, disclosure or > distribution is prohibited. If you are not the intended recipient, please > contact the sender by reply e-mail and destroy all copies of the original > message. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
