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Subject: [genome] Thanks/Suggestion
Posted by Artur Jaroszewicz on Tue, 14 May 2013 23:06:02 GMT
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Hello there,
Firstly, thank you for all you do. Your service is completely invaluable in
my line of work (RNA seq), and you make my job much, much easier.
Secondly, as I use your site a lot, I wanted to propose a new track for
your table browser: canonical pathways such as WNT, BMP, Notch, Hedgehog,
etc. I think it would add a lot of utility to a service that is mostly
there.
Thank you again,
Artur Jaroszewicz
Matteo Pellegrini Lab
UCLA
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Subject: Re: [genome] Thanks/Suggestion
Posted by Brian Lee on Thu, 16 May 2013 18:07:01 GMT
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Dear Artur Jaroszewicz,
Thank you for your kind comments, for using the UCSC Genome Browser, and
for your proposal about a new track. We would be interested to know more
about what exactly you are imagining, as your feedback is highly valued.
You may be interested to learn that we have accesses to pathways from our
gene details page, for example if you were to navigate in the browser to
the position of the gene p53 and click it, you would come to p53's details
page: http://genome.ucsc.edu/cgi-bin/hgGene?db=hg19&hgg_gene=p 53
On the gene details page you can click the highlighted "Pathways" link, and
you will jump down to the lower section of the page, which includes links
out to various pathways:
http://genome.ucsc.edu/cgi-bin/hgGene?db=hg19&hgg_gene=p 53#pathways
In the Table Browser, these tables are located under the UCSC genes track
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in the bioCycPathway, cgapBiocPathway and keggPathway tables. More
information about these tables is included in the associated bioCycMapDesc,
cgapBiocDesc, and keggMapDesc description tables.
You can explore them in the table browser by making the following
selections:
Clade: Mammal
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Prediction Tracks
Track: UCSC Genes
Table: bioCycPathway
Then click the "describe schema" button to see what values are contained.
If you scroll down to the connected Tables and Joining Fields section, you
can click on the related bioCycMapDesc table, and then see sample rows of
the matching mapID and description, such as "ALANINE-SYN2-PWY | alanine
biosynthesis II".
Again, thank you for your input and using the UCSC Genome Browser. Please
respond with more information about what you may be envisioning as a
possible future feature that could be of interest, if this existing pathway
information was not of the source you were imagining. Also, if you have
any further questions, please feel free to contact the mailing list again
at [email protected].
All the best,
Brian Lee
UCSC Genome Bioinformatics Group
On Tue, May 14, 2013 at 4:06 PM, Artur Jaroszewicz <[email protected]>wrote:
> Hello there,
>
> Firstly, thank you for all you do. Your service is completely invaluable
> in my line of work (RNA seq), and you make my job much, much easier.
> Secondly, as I use your site a lot, I wanted to propose a new track for
> your table browser: canonical pathways such as WNT, BMP, Notch, Hedgehog,
> etc. I think it would add a lot of utility to a service that is mostly
> there.
>
> Thank you again,
>
> Artur Jaroszewicz
> Matteo Pellegrini Lab
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> UCLA
>
> ->
>
>
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