[Genome] how to get human protein mapped by tBlastn?

[Pauline Fujita]

Hello Xianjun,

The human proteins track uses the table you mentioned, blastHg18KG, to 
look up the identifiers of human proteins that align to a given region 
of the zebrafish genome. These identifiers are listed in the column 
"qName" of the blastHg18KG table. In your example, the identifiers 
associated with the region chr14:4,399,990-4,421,902 are:

M19154
NM_003238
BC096236

The browser retrieves the geneIds of these identifiers from the table 
"blastKGRef04" in the human, Mar 2006 (hg18) assembly. Normally, when 
you click on the "describe table schema" button, in addition to 
describing the table, all the related tables are listed. Unfortunately, 
we do not list related tables from assemblies in *other* organisms, and 
so you will not see this second table listed in the usual place.

To retrieve the IDs you are looking for, select in the table browser:

   clade: vertebrate
   genome: zebrafish
   assembly: July 2007
   group: All Tables
   database: danRer5
   table: blastHg18KG
   region: click "position" and paste in the region you are interested 
in searching
   output format: selected fields from primary and related tables

then click on "get output". This will take you to a menu where you can 
select which columns you want to appear in the output. Select "qName" 
and click "get output".

This should output all the identifiers as a text list. Copy this list, 
then return to the main table browser menu. Now select:

   clade: vertebrate
   genome: human
   assembly: Mar 2006
   group: All Tables
   database: hg18
   table: blastKGRef04
   region: click "genome"
   output format: selected fields from primary and related tables
   identifiers: click on "paste list" then paste the list of identifiers 
from zebrafish into the textbox and click "submit"

Then click on "get output" and in the "select fields from 
hg18.blastKGRef04" section, click on "geneId". Finally, click on "get 
output" and this should give the list of protein names you are looking for.

Hopefully this information was helpful and answers your question. If you 
have further questions or require clarification feel free to contact the 
mailing list at genome at soe.ucsc.edu <mailto:genome at soe.ucsc.edu>.

Regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

Xianjun Dong wrote:
> hi,
>
> I want to get the human protein name mapped by tBlastn in another genome 
> browser? For example, when looking chr14:4,399,990-4,421,902 in 
> zebrafish, it's mapped to human protein TGFB2 in the track of "Human 
> Protein Mapped by Chained tBlastn". How can I get the name of 'TGFB2' by 
> query some table?
>
> I looked into the schema of table blastHg18KG, which only has info of 
> human mRNA mapped. From mRNA to protein info displaying on the track, 
> where did you get the data?
>
> Regards,
>
>