[Genome] A question about UCSC genome brower

[Fan Hsu]

Hi Jian You,

The way we generated GO related annotation with UCSC Known Genes
is based on using GO/UniProt association data downloaded from:

ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/gene_association.goa_unipro
t.gz

which seems to provide more comprehensive result.

We have recently updated our go database and it will be released
to our public servers soon.  For this particular
gene (NM_015035/ZHX3_HUMAN), the new GO data indicate 13 related GO terms:

GO:0003676
GO:0003677
GO:0003700
GO:0005515
GO:0005622
GO:0005634
GO:0006350
GO:0006355
GO:0008270
GO:0043565
GO:0045449
GO:0045892
GO:0046872

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
Behalf Of liaojy
Sent: Friday, February 09, 2007 2:55 AM
To: genome at soe.ucsc.edu
Subject: [Genome] A question about UCSC genome brower


Hi,
         I encounter a problem when I used UCSC genome browser. I
searched ZHX3 gene in human genome, and then entered the "Human Gene
ZHX3 Description and Page Index" PAGE (URL:
http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=NM_015035
<http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=NM_015035&hgg_prot=ZHX3_
HUMAN&hgg_chrom=chr20&hgg_start=39240502&hgg_end=39362153&hgg_type=known
Gene&db=hg18&hgsid=85816915%20TITLE>
&hgg_prot=ZHX3_HUMAN&hgg_chrom=chr20&hgg_start=39240502&hgg_end=39362153
&hgg_type=knownGene&db=hg18&hgsid=85816915%20TITLE=). In "Gene Ontology
(GO) Annotations with Structured Vocabulary", it has 12 GO terms. I
searched ZHX3 in GO database(http://www.godatabase.org
<http://www.godatabase.org/> ), I only got 4 terms, they were
"nucleus","protein binding","transcription factor activity","negative
regulation of transcription, DNA-dependent", Why GO database search
result is inconsistent with UCSC genome brower result?

Sincerely,
Liaojianyou
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