[Genome] Gene Ontology

[Fan Hsu]

Thanks to Pete pointing out that acc is the UniProt accession, which you can
bet from the hg18.kgXref table.

To figure out hierarchy, you need to do a little bit of your own
programming/processing.  The parent/child info I believe is contained in the
term2term table of the go database.

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu] On
Behalf Of Pete Shepard
Sent: Friday, 11 January, 2008 8:36 AM
To: J.Bowes at manchester.ac.uk
Cc: genome at soe.ucsc.edu
Subject: Re: [Genome] Gene Ontology

Hi John,

I can try to field this one while you wait for the experts because I have
been working on this exact problem.

You first need to convert your gene id to what I think is a uniprot/tremble
id. Then you can go to the table browser group:  and select all tables, then
from database: select "go"and go.goaPart as the table:. Paste the
uniprot/tremble id into the identifiers (names/accessions): field. Select
"selected fields from primary and related tables" from the output format:
field and hit get output. Now scroll down to linked tables and select "go"
then scroll all the way down and hit "allow selection from checked tables"
select check "name", "term type", and "acc" from the go.term field and then
h
it get output. Below is what I get for your gene. One thing that I cannot
find  is  a way to get the  hierarchical levels of these terms if you find
this out please let me know.

Peter


#go.goaPart.dbObjectId	go.goaPart.dbObjectSymbol	go.term.name
go.term.term_type	go.term.acc
Q9Y2R2	PTN22_HUMAN	phosphoprotein phosphatase
activity	molecular_function	GO:0004721
Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase
activity	molecular_function	GO:0004725
Q9Y2R2	PTN22_HUMAN	protein amino acid
dephosphorylation	biological_process	GO:0006470
Q9Y2R2	PTN22_HUMAN	signal transduction	biological_process
GO:0007165
Q9Y2R2	PTN22_HUMAN	development	biological_process	GO:0007275
Q9Y2R2	PTN22_HUMAN	hydrolase activity	molecular_function
GO:0016787






On Jan 11, 2008 6:35 AM, John Bowes <J.Bowes at manchester.ac.uk> wrote:

> Hello,
>
> I have spent a number of hours trying (unsuccessfully) to extract GO data
> from for particular gene ids. My aim is to supply a list of gene ids, e.g.
> PTPN22, and extract the three GO aspects (biological_process,
> cellular_component and molecular_function). I have tried a number of
times,
> but do not get useful data (either no data, or a large volume of multiple
> entries). I am sure this due to me not fully understanding the table
> relationships. I have looked at related questions in the archives but
could
> not implement them.
>
> One example would be PTPN22, this has two molecular_function and three
> biological_processes when GO is searched manually. But I can't reproduce
> this through the UCSC browser. Any help would be greatly appreciated.
>
> You are doing a great job with this browser.
>
> Thank you.
>
> John Bowes
>
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>
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