Hi Sigal, This data is fairly old - there should really not be any reason to use it anymore. Also, UCSC Genes and Known Genes were created by different processes and are not appropriate for direct comparisons.
Even so, I did look for a table with kgColor-like data when you originally asked and but was not able to identify a table for the Known Gene builds (which is why I just sent the HTML description). In the background I started gathering input from some other team members to see if they have any information about this type of data. We will get back to you if there is a table with the data. Thanks, Jennifer On 5/3/10 4:09 PM, Sigal Blay wrote: > Thanks Jennifer, > but I'm querying the colors remotely by retrieving the database tables and not > through an internet browser. > I was able to determine gene colors with the information in the > kgColor table for "hg19", "hg18". > But earlier assemblies don't have the kgColor table. > Is there a different table for the earlier assemblies where gene colors are > specified? > > Thanks, > Sigal > > On Mon, May 03, 2010 at 02:45:04PM -0700, Jennifer Jackson wrote: >> Hello Sigal, >> >> Color coding is defined in the Known Genes track description page, >> in the second section under "Methods". See the actual html page for >> the links out to additional information. >> >> Display Conventions and Configuration >> >> This track follows the display conventions for gene prediction >> tracks with the following color scheme: >> >> Black: indicates the gene has a corresponding entry in the Protein >> Databank (PDB). >> Dark Blue: indicates the gene has either a corresponding RefSeq mRNA >> that is "Reviewed" or "Validated" or a corresponding Swiss-Prot >> protein. >> Medium Blue: indicates the gene has a corresponding RefSeq mRNA that >> is not "Reviewed" nor "Validated". >> Light Blue: everything else. That is, the gene does not have a >> corresponding Protein Databank entry, RefSeq mRNA, or Swiss-Prot >> protein, but it has supporting evidence of a GenBank mRNA with a >> UniProt (TrEMBL) protein. >> >> This track contains an optional codon coloring feature that allows >> users to quickly validate and compare gene predictions. To display >> codon colors, select the genomic codons option from the Color track >> by codons pull-down menu. Click here for more information about this >> feature. >> >> Thanks, >> Jennifer >> >> --------------------------------- >> Jennifer Jackson >> UCSC Genome Informatics Group >> http://genome.ucsc.edu/ >> >> On 5/3/10 2:29 PM, Sigal Blay wrote: >>> The color coding is contained in the UCSC Gene track associated >>> table "kgColor" for hg19 and hg18. >>> what about earlier assemblies? >>> >>> Thanks! >>> Sigal _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
