Hello again Gue Su,
To match a UCSC (knownGene) identifier using the table browser you need
to use the mm9.kgXref and the proteome.hgnc tables as follows. Select
mm9 and then select:
group: Genes and Gene Prediction Tracks
track: UCSC Genes
table: kgXref
identifiers: click on "paste list" to input UCSC identifiers
(i.e.
uc007aet.1)
output format: "selected fields from primary and related tables"
Once you click on "get output" this will take you to a menu where you
can specify which fields you want to retrieve from kgXref. Now check the
box beside proteome hgnc and click on "allow selection from checked
tables" then you should be able to select MgdId from the proteome.hgnc
fields.
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 [email protected].
Regards,
Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
Gue Su Chang wrote:
> Dear UCSC browser;
>
> Hello, this is Gue-Su Chang again. I almost figured out my second question
> as below. I have a question related with it. How can I match the UCSC gene
> identity name (like "uc007aet.1", "uc007afn.1") to the MGI accession ID
> (like "MGI:3528744")?
>
> I will greatly appreciate it if you could help me out. Thanks a lot.
>
> Best
> Gue SU
>
> -----Original Message-----
> From: Gue Su Chang [mailto:[email protected]]
> Sent: Tuesday, July 14, 2009 1:08 PM
> To: '[email protected]'
> Subject: A question about UCSC tables
>
> Dear UCSC browser;
>
> Hello, this is Gue-Su Chang. I am a graduate student at Penn State and I am
> working with Dr. Pugh in Wartik. May I ask several questions?
>
> Recently, I am using the UCSC Table browser to curate known genes from the
> mouse genome. I chose "UCSC Genes" track and the "knownGene" table. The
> following lines are a result example I now have. I would like to ask a
> question about them.
>
> -----------------------------------
> uc007afy.1 chr1 + 6720131 6851021 6758978 6848681 24
> 6720131,6727660,6742376,6743074,6758978,6761024,6785466,6792400,6797623,6799
> 357,6800654,6807683,6810014,6817856,6823643,6832219,6832953,6834201,6834371,
> 6835651,6838987,6845449,6847380,6848540,
> 6720321,6727738,6742449,6743117,6759033,6761055,6785657,6793186,6797758,6799
> 448,6800759,6807877,6810226,6818102,6823759,6832282,6833022,6834264,6834452,
> 6835873,6839076,6845553,6847524,6851021, Q80TY4 uc007afy.1
>
> uc007afz.1 chr1 + 6720131 6851021 6758978 6848681 23
> 6720131,6742376,6743074,6758978,6761024,6785466,6792400,6797623,6799357,6800
> 654,6807683,6810014,6817856,6823643,6832219,6832953,6834201,6834371,6835651,
> 6838987,6845449,6847380,6848540,
> 6720321,6742449,6743117,6759033,6761055,6785657,6793186,6797758,6799448,6800
> 759,6807877,6810226,6818102,6823759,6832282,6833022,6834264,6834452,6835873,
> 6839076,6845553,6847524,6851021, Q80TY4 uc007afz.1
> -----------------------------------
>
> Two questions are here, and it will be greatly appreciated if you could
> provide answers for me.
>
> (1) They are two isoforms of a protein which are processed differently by
> alternative splicing. Why do they have the same protein ID, like "Q80TY4"?
> They clearly consist of different exons.
>
> (2) I saw their ID names are "uc007afy.1" and "uc007afz.1". I would like to
> have their common names which are more familar with people. How can I
> retrieve this kind of information from UCSC?
>
> I am looking forward to your kind help.
>
> Best regards,
> Gue Su
>
>
> ----------------------------------------------------------------------
> Chang, Gue Su (E-mail: [email protected])
>
> Graduate student
> IBIOS Graduate Program Option in Bioinformatics and Genomics
> http://www.huck.psu.edu/IBIOS/
>
> PI: Dr. Frank B. Pugh
> Center for Eukaryotic Gene Regulation
> 331 South Frear
> Pennsylvania State University
> University Park PA, 16802
>
> http://www.bmb.psu.edu/faculty/pugh/pugh.html
> ----------------------------------------------------------------------
>
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
