[Genome] GO annotation

[Jay an]

hello Brooke,
   
  your instruction is very helpful. thanks
  GO can be categorized different processes, such as physiological process, metabolism, cellular physiological process.
  how can get this information from UCSC ?
  regards
   
  Jay
  


Brooke Rhead <rhead at soe.ucsc.edu> wrote:
  Hi Jay,

The go.dbObjectId is the UniProt accession number. (But in the case of 
A0A000, the species is not human, but Streptomyces ghanaensis [TaxID: 
35758]).

The go database contains dbObjectId's for all assemblies, not just hg18. 
However, it is possible to distingush species in the goaPart table, as 
the species name is included as part of the dbObjectSymbol field. Here 
are some examples where "HUMAN" is included:

mysql> select * from goaPart where dbObjectSymbol like '%_HUMAN' limit 5;
+------------+----------------+-------+------------+--------+
| dbObjectId | dbObjectSymbol | notId | goId | aspect |
+------------+----------------+-------+------------+--------+
| A0A184 | A0A184_HUMAN | | GO:0005764 | C |
| A0A184 | A0A184_HUMAN | | GO:0006629 | P |
| A0A184 | A0A184_HUMAN | | GO:0006665 | P |
| A0A1K6 | A0A1K6_HUMAN | | GO:0004222 | F |
| A0A1K6 | A0A1K6_HUMAN | | GO:0006508 | P |
+------------+----------------+-------+------------+--------+
5 rows in set (0.00 sec)

You can use the Table Browser to filter the goaPart table so that only 
human UniProt IDs are shown. To do this, hit the filter "create" 
button. In the free-form query box enter the text:

dbObjectSymbol like '%HUMAN'

and hit "submit". The output should be limited to only the UniProt 
symbols with "HUMAN" in the name.

The filtered goaPart table may be all you need to map GO accessions to 
genes. But, as you have noticed, the goaPart table is linked to the 
hg18 kgXref table, too. If you would like to get the gene names 
corresponding to GO accessions from kgXref, you can do that, too, with 
the Table Browser:

1. You will likely want to leave the filter on the goaPart table in 
place (dbObjectSymbol like '%HUMAN').

2. Select the option for "output format: selected fields from primary 
and related tables" and hit "get output".

3. On the next screen, under the "Linked Tables" heading, select the box 
for the hg18 kgXref table. Scroll to the bottom of the page and hit 
"Allow selection from checked tables".

4. You should now see a section called at the top of the page called 
"hg18.kgXref fields", where you can select any of the identifiers from 
the kgXref table (like gene symbol).

5. Hit "get output". You should get a list of GO identifiers with 
associated gene names from kgXref. Keep in mind that not every GO ID 
will be associated with a gene in the kgXref table.

I hope this information helps.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Jay an wrote:
> thanks Brooke,
> 
> I followed you instruction. but I got below:
> 
> #dbObjectId dbObjectSymbol notId goId aspect
> A0A000 A0A000_9ACTO GO:0003870 F
> A0A000 A0A000_9ACTO GO:0006783 P
> A0A000 A0A000_9ACTO GO:0009058 P
> 
> there is not proteinID.
> I found "hg18.kgXref 
> .spID 
> (via goaPart.dbObjectId",
> how can I "via goaPart.dbObjectId"?
> 
> thank you
> Jay
> 
> 
> 
> */Brooke Rhead /* wrote:
> 
> Hello Jay,
> 
> The GO accessions are linked to genes (that is, protein IDs) in the
> table 'goaPart', which resides in our 'go' database.
> 
> You can get to this table in the Table Browser by selecting "group: all
> tables" and "database: go", then selecting "table: go.goaPart".
> 
> I hope this information helps. If you have further questions, please
> feel free to write back to this list.
> 
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
> 
> 
> Jay an wrote:
> > hello,
> >
> > every GO:XXXXX has related genes. can you tell me how to a matrix
> > (GO:XXXXX and genes)?
> >
> >
> > thanks
> >
> >
> >
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