[Genome] gnf to ensemble IDs

[sonja althammer]

hello again!
sorry for asking again! i found the data i wanted for mouse but just by following your history.. when i follow the description (group:  Genes and Gene Prediction Tracks;  track: Ensembl Genes;  table: ensGene)
i get a different table: 
that looks like:

#name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds
ENSMUST00000097835.1 chr1 + 3044313 3044814 3044313 3044814 1 3044313, 3044814,
i dont understand why...
so that is the problem i have now by receiving the same data for human...
can you tell me what am i doing wrong?
best regards!
sonja

sonja althammer <sonjalthammer at yahoo.com> wrote: hello!
i cannot find the table "knownToGnf1m". your description was:

group: Expression and Regulation; track: GNF Atlas2; table: knownToGnf1m

probably it is because i cannot  find where to select the database mm8 (Feb 
2006)
i was using assembly march 2006.
where can i select the database?
best regards!
sonja

Kayla Smith <kayla at soe.ucsc.edu> wrote: 
Hello Sonja,

The answer to your question will involve using a program called Galaxy, 
available here:
http://main.g2.bx.psu.edu/

Here is the method to associate the two pieces of data that you are 
looking for.

1.  Click on the "Get Data" button on the left-hand side of the Galaxy 
main page.   Then click on "UCSC Main".  You'll be using the mm8 (Feb 
2006) database to get two tables.  The first table  is:

group: Expression and Regulation; track: GNF Atlas2; table: knownToGnf1m

The second table is:

group:  Genes and Gene Prediction Tracks;  track: Ensembl Genes;  table: 
ensGene

In both cases, you'll want to make sure that the "send output to Galaxy" 
box is checked, and click "get output".

2.  Once you have loaded those tables into Galaxy, click on the "Join, 
Subtract and Group" link on the left-hand side of the page.  Then click 
on "join two queries".

Use the drop down menus to select column 1 of each of your tables.

Click "execute".

Your output will be an association of the ensembl ids and the gnf ids.

In particular, if you search the output for your "gnf1m09364_a_at", 
you'll find this line:

NM_175370 ENSMUST00000055313.5 NM_175370 gnf1m09364_a_at

If you want to save yourself some trouble, you can look at my saved 
Galaxy history  here:
http://main.g2.bx.psu.edu/history_import?id=147644

I hope this information is helpful to you.  Please don't hesitate to 
contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group


sonja althammer wrote:
> Hello!
> I am working with the gnf atlas for expression data where i get gene-names like :
> 
> gnf1m09364_a_at
> 
> Can you tell me, how to derive the ENSEMBLE Gene IDs like ENSG00000146556 from them?
> 
> Best regards!
> Sonja
>        
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