[Genome] GO annotation

[Jay an]

Hi Brooke,
 
I got a table consisting of GO:XXX and gene symbol.
but I found many gene symbols
are "n/a". what does it mean?

sample:
#go.goaPart.goId	go.goaPart.aspect	go.term.id
hg18.kgXref.geneSymbol
GO:0006915	P	4835	n/a
GO:0007050	P	4966	n/a
GO:0008284	P	5785	n/a
GO:0005515	F	3520	ITGB1BP1
GO:0007155	P	5063	ITGB1BP1
GO:0007160	P	5068	ITGB1BP1
GO:0007243	P	5149	ITGB1BP1
GO:0008022	F	5544	ITGB1BP1
GO:0016020	C	8812	ITGB1BP1
GO:0005643	C	3640	n/a
GO:0008150	P	5662	n/a



 
 
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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