Hello,
I have a correction from one of the scientists that created the track. Going
through UCSC Genes is not the best option. Here is his advice:
-----
select ccdsInfo.ccds, refSeqSummary.summary from ccdsInfo,
refSeqSummary where
substring(ccdsInfo.mrnaAcc,1,locate(".",ccdsInfo.mrnaAcc)-1) =
refSeqSummary.mrnaAcc;
however, information will not be return for all CCDS because:
- refSeqSummary on contains information for reviewed refseqs
- some refseqs may have been deleted since CCDS was created.
-----
Sorry for the confusion and hope this works out for you,
Jennifer
------------------------------------------------
Jennifer Jackson
UCSC Genome Bioinformatics Group
----- "Jennifer Jackson" <[email protected]> wrote:
> From: "Jennifer Jackson" <[email protected]>
> To: "Jeffrey Rosenfeld" <[email protected]>
> Cc: [email protected]
> Sent: Friday, August 21, 2009 3:11:20 PM GMT -08:00 US/Canada Pacific
> Subject: Re: [Genome] CCDs gene names and descriptions
>
> Hello,
>
> The CCDS records are not named with RefSeq identifiers. They are
> composite sequences derived from multiple sources. They are however
> linked into the UCSC Genes track, which could be used as a link to
> other sources (gene name, symbol, refseq accession, etc.)
>
> The Table browser would be a good tool for you to explore. You can use
> it for queries or simply find out schema information (table contents,
> data examples/format, common keys to join on) in order to build
> successful mysql queries.
>
> How to do this: from main browser web page click on "Tables". Then
> adjust clade, genome, etc. all the way down to track = CCDS. For the
> default (primary) table, click on "describe table schema". This is
> your information page. Schema at the top, linked tables (including
> which key is the link to join with), and track description on the
> bottom.
>
> To link from CCDS to UCSC Genes, start with the CCDS track's primary
> table and link through ccdsKgMap. In the second table is the
> transcript identifier for the UCSC Genes transcripts. Use this to
> obtain gene name/symbol information from the kgAlias or kgXref tables
> or refLink (to start with, there are others to select from, explore to
> see if useful for you).
>
> We hope this helps,
> Jennifer
>
> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser
>
> ------------------------------------------------
> Jennifer Jackson
> UCSC Genome Bioinformatics Group
>
> ----- "Jeffrey Rosenfeld" <[email protected]> wrote:
>
> > From: "Jeffrey Rosenfeld" <[email protected]>
> > To: [email protected]
> > Sent: Friday, August 21, 2009 11:18:04 AM GMT -08:00 US/Canada
> Pacific
> > Subject: [Genome] CCDs gene names and descriptions
> >
> > Hi,
> >
> > I have been looking at your database without success and I was
> > hoping
> > you could help me. I am trying to get a list of all of the CCDS
> gene
> > IDs along with the gene names and gene descriptions. I thought
> that
> > a
> > merge of ccdsInfo and refSeqSummary would allow be to link up the
> > mRNA
> > description with the summary, but the following MySQL query on your
> > server turned up nothing:
> > select ccdsInfo.ccds, refSeqSummary.summary from ccdsInfo,
> > refSeqSummary
> > where ccdsInfo.mrnaAcc = refSeqSummary.mrnaAcc;
> > Empty set (1.11 sec)
> >
> > indicating that there is a disconnect between the tables. Is there
> a
> > proper way to perform this query, or could you just send me a
> table?
> >
> > Thank you for the help,
> >
> > Jeff
> >
> >
> > --
> >
> > Jeffrey Rosenfeld Ph. D.
> >
> > Research Scientist
> > Laboratory of Analytic Genomics, Division of Psychiatry Research,
> > The Zucker Hillside Hospital;
> >
> > North Shore - Long Island Jewish Health System;
> >
> > Mailing Address:
> > The Zucker Hillside Hospital
> > Psychiatry Research
> > 75-59 263rd Street
> > Glen Oaks, NY 11004
> >
> > 718-470-8836 (ph)
> > 718-343-1659 (fax)
> >
> > _______________________________________________
> > 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
