[Genome] orthologous genes

[Rachel Harte]

Jay an,

Unfortunately, we don't have a table that looks exactly as you describe
but you should be able to get this information from the *BlastTab tables.
If you look for the *BlastTab tables, for example, in human hg18 then you
would find the mmBlastTab, rnBlastTab, drBlastTab etc. The query is the
human gene from the UCSC Genes set (knownGene table) and the target is the
gene in the known genes set of the other species. For mouse and rat, it
is Known Genes, for zebrafish it is Ensembl Genes, for C. elegans it is
Sanger Genes (sangerGene).

Example:
For the gene, uc001aci.1, from the Human UCSC Genes, the rat ortholog can
be found in the rnBlastTab table in hg18.
Human (query) Rat (Target)
uc001aci.1    NM_024360

Then look up uc001aci.1 as query in mmBlastTab:
Mouse (Target)
NM_008235

Therefore this gives:
Human (query) Rat (Target) Mouse (Target)
uc001aci.1    NM_024360   NM_008235     ....

and so you can look for this query across all the *BlastTab tables and
build up your own table as above.

For the human hg18 UCSC Genes (knownGene table), the Genbank mRNAs
corresponding to the IDs (e.g. uc001aci.1 as for the query above) may be
found in the kgXref table. The ID is the kgID:

mysql>select * from kgXref where kgID = "uc001aci.1";
+------------+-----------+--------+-------------+------------+-----------+-----------+-------------------------------+
| kgID       | mRNA      | spID   | spDisplayID | geneSymbol | refseq    |
protAcc   | description                   |
+------------+-----------+--------+-------------+------------+-----------+-----------+-------------------------------+
| uc001aci.1 | NM_021170 | Q9HCC6 | HES4_HUMAN  | HES4       | NM_021170 |
NP_066993 | hairy and enhancer of split 4 |
+------------+-----------+--------+-------------+------------+-----------+-----------+-------------------------------+

You can query all these tables through the Table Browser (click on the
Tables link on the top blue bar). Also if you have MySQL client
libraries installed, you can use MySQL to directly query our databases,
see this link for more details:

http://genome.ucsc.edu/FAQ/FAQdownloads#download29

Rachel


 Rachel
Harte UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Mon, 30 Apr 2007, Jay an wrote:

> thank you Rachel,
>
>   I have looked the table you advised. but It's slightly different with what I wanted.
>   I hope a table whose columns correspond species. each row consists of
>   orthologous genes of corresponding to species.
>
>   Jay
>
>
>
>
> Rachel Harte <hartera at soe.ucsc.edu> wrote:
>   Hello Jay an,
>
> You can download these tables either through the Table Browser (Tables
> link on the top blue bar) or through our downloads server:
>
> http://hgdownload.cse.ucsc.edu
>
> Just click on the organism of interest and then find the appropriate
> assembly, then click on the Annotation database link. From here, you
> can download the tables. The tables are called *BlastTab:
> mmBlastTab - mouse
> ceBlastTab - worm
> dmBlastTab - drosophila
> drBlastTab - zebrafish
> humanBlastTab or hgBlastTab - human
> rnBlastTab - rat
> scBlastTab - yeast
>
> I hope that this helps you. Please let us know if you have further
> questions.
>
> Rachel
>
> Rachel Harte
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
>
> On Mon, 30 Apr 2007, Jay an wrote:
>
> > hello,
> >
> > could you tell me how to download the table about orthologous gene names in human, mouse and rat as below?
> >
> > | human | mouse | rat |
> > | NM_XXXXX | NM_XXXXXX | NM_XXXXX |
> > |... | | |
> >
> >
> >
> >
> > ---------------------------------
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> > Check outnew cars at Yahoo! Autos.
> > _______________________________________________
> > Genome maillist - Genome at soe.ucsc.edu
> > http://www.soe.ucsc.edu/mailman/listinfo/genome
> >
>
>
>
> ---------------------------------
> Ahhh...imagining that irresistible "new car" smell?
>  Check outnew cars at Yahoo! Autos.