Dear Anton,
You will want to set the table to "refFlat" instead of table "refGene".
For the selected fields you will want to check these:
geneName Name of gene as it appears in genome browser.
name Name of gene
If you have further questions, please contact the mailing list.
Vanessa Kirkup Swing
UCSC Genome Bioinformatics Grouo
----- Original Message -----
From: "Anton Kratz" <[email protected]>
To: "UCSC Genome Browser Help Desk" <[email protected]>
Sent: Thursday, October 28, 2010 1:35:30 AM GMT -08:00 US/Canada Pacific
Subject: [Genome] missing connection between RefSeq ID and gene symbol,
possibly more missing?
Dear UCSC team,
I tried to construct a table using the Table Browser which contains RefSeq
genes and their correspoding gene symbols (how I did this, please see
below).
I am working with rat, rn4 assembly.
In the resulting table, I do not find the string "Camk2a", a gene which I am
interested in. However, when I search for Camk2a in the "gene" search box
(right next to the "positrin/search" box) of the Genome Browser on Rat Nov.
2004 (Baylor 3.4/rn4) Assembly, and then click on "jump", I get a hit:
*RefSeq Genes
Camk2a at chr18:56879247-56948537 - (NM_012920) calcium/calmodulin-dependent
protein kinase type*
This is the gene I am searching for. However, in the table generated with
the table browser there is no connection NM_012920 --> Camk2a. It just lists
"NM_012920 n/a".
Could you please shed some light on how gene identifiers are mapped here?
How can I make a table which contains the link between NM_012920 --> Camk2a,
and does the workflow I am using now mean that there are other connections
which I am missing?
Thanks!
Anton
P.S.: This is how I constructed my table connecting #rn4.refGene.name and
rn4.kgXref.geneSymbol:
assembly "Nov. 2004 (Baylor 3.4/rn4)"
group "Genes and Gene Prediction Tracks", track "RefSeq Genes"
table "refGene"
"selected fields from primary and selected tables"
get output
-->
Select Fields from rn4.refGene
CHECK name Name of gene
Linked Tables
CHECK rn4 kgXref Link together a Known Gene ID and a gene alias
-->
rn4.kgXref fields
CHECK geneSymbol Gene Symbol
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
