Hi Margaret, We released a new UCSC Genes set a couple of weeks ago (see: http://genome.ucsc.edu/goldenPath/newsarch.html#020212), and the naming issue with MYC has been corrected.
Thank you for your bug report. It was helped us improve the transcript-naming part of our UCSC Genes pipeline. -- Brooke Rhead UCSC Genome Bioinformatics Group On 2/4/11 2:26 PM, Brooke Rhead wrote: > Hello Margaret, > > It looks like you have detected a bug in the UCSC Genes pipeline. The > bug has been documented, and we will look at the issue and incorporate a > fix into the next UCSC Genes build. > > Thank you very much for bringing this to our attention! > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 02/03/11 18:33, Brooke Rhead wrote: >> Hi Margaret, >> >> Our mailing list software strips attachments, so I never saw your >> screen shot. But I see what you are saying. This UCSC Genes track >> shows MYC in hg19, but everywhere else (previous assemblies and other >> tracks in hg19, like RefSeq) the same transcripts are labeled PVT1. >> >> I have asked one of the engineers here who works on UCSC Genes what >> might be going on in this case. I'll let you know what she says. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> On 02/03/11 07:45, [email protected] wrote: >>> If you search for "MYC" in the HG browser/gateway, the first 3 hits >> listed in Hg19 are transcripts of what was labeled PVT1 in Hg18 & all >> earlier versions. This matches the gene labels for UCSC & RefSeq tracks >> in Hg19, as shown in the screen shot attached to my original query. What >> is the status of PVT1? Last I heard it wasn't MYC. >>> ---------------------------------------------------- >>> >>> Margaret Leversha, PhD >>> MSKCC >>> >>> -----Original Message----- >>> From: Brooke Rhead [mailto:[email protected]] Sent: Thursday, >>> February 03, 2011 12:21 AM >>> To: Leversha, Margaret A./Sloan-Kettering Institute >>> Cc: [email protected] >>> Subject: Re: [Genome] PVT1 now displays as MYC >>> >>> Hi Margaret, >>> >>> Which track are you referring to? Is it UCSC Genes / Known Genes? >>> >>> I'm looking in these regions: >>> >>> hg17: chr8:128,569,240-129,489,402 >>> hg18: chr8:128,569,240-129,489,402 >>> hg19: chr8:128,500,058-129,420,220 >>> >>> For hg17, PVT1 is not annotated at all in the Known Genes track (on >>> hg17, only protein-coding genes were annotated). >>> >>> I do see that what was called PVT1 in the hg18 UCSC Genes track is >>> called MYC in hg19. I don't have an immediate explanation for that, >>> but I could ask the developers of the UCSC Genes track. Is that what >>> you are referring to? >>> >>> Please reply to [email protected] and let us know which track, and >>> we can try to give you more information. >>> >>> -- >>> Brooke Rhead >>> UCSC Genome Bioinformatics Group >>> >>> >>> >>> On 01/31/11 15:17, [email protected] wrote: >>>> Is there a reason for the name switch for PVT1 (adjacent to MYC in >>> 8q24) in earlier builds to MYC in Hg17? >>>> ---------------------------------------------------- >>>> >>>> Margaret Leversha, PhD >>>> MSKCC >>>> >>>> >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> _______________________________________________ >>>> Genome maillist - [email protected] >>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
