Hello Sigal, As you may have found, the color coding is described in the UCSC genes track description page:
Display Conventions and Configuration <omitted text> The following color key is used: Black -- feature has a corresponding entry in the Protein Data Bank (PDB) Dark blue -- transcript has been reviewed or validated by either the RefSeq, SwissProt or CCDS staff Medium blue -- other RefSeq transcripts Light blue -- non-RefSeq transcripts The color coding is contained in the UCSC Gene track associated table "kgColor". By examining a mix of the three RGB values, the color can be matched to the browser display and the transcript's associated evidence level in the track description. Summary for hg19: mysql> select count(*), r, g, b from kgColor group by r, g, b; +----------+-----+-----+-----+ | count(*) | r | g | b | +----------+-----+-----+-----+ | 3434 | 0 | 0 | 0 | = black | 23567 | 12 | 12 | 120 | = dark blue | 3346 | 80 | 80 | 160 | = medium blue | 47267 | 130 | 130 | 210 | = light blue +----------+-----+-----+-----+ Examining other associated tables and what data they contain can help to dig deeper to find out about supporting evidence. In particular, kgXref contains quick summary information. Open the Table browser to the UCSC Genes track and click on "describe table schema" with knownGene (the primary table) selected to view a complete list of associated tables and joining keys. We hope this is helpful! Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/19/10 9:51 PM, Sigal Blay wrote: > This is in regard to the color key for the UCSC Genes Track > http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownGene > > How can one determine the gene appropriate color > (Black, Dark blue, medium blue, light blue) > from the associated db tables in the Genes and Gene Prediction Tracks? > > Thanks, > > Sigal > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
