[Genome] HPRD data in GeneSorter

[Brett Abrahams]

Hi Gail,

I was hoping you might be able to answer a follow-up question
regarding a specific example - UBE3C (aka uc001hbr.1).

Using HRPD, and limiting the distance score to 1.5 or less, I observe
seven interactors (see attached and
http://genome.ucsc.edu/cgi-bin/hgNear?hgsid=106065993).

When I go directly to the HPRD, however, only four interactions are
reported and none of these overlap with those listed on the UCSC site.
http://www.hprd.org/interactions?protein=15604&isoform_id=15604_1&isoform_name=

I've look through the faqs and the 2 references listed on the HPRD
site but nothing seems to clear things up. I love this tool (and your
link to the data) but do want to make sure I know what the output
means. Any thoughts would be much appreciated. Thanks in advance.

-b

On Fri, Jan 11, 2008 at 5:03 PM, Galt Barber <galt at soe.ucsc.edu> wrote:
>
>  If you are interested in the HPRD P2P interaction distance column,
>  you can see it's desciption page here:
>
>  http://genome.ucsc.edu/cgi-bin/hgNear?hgsid=102348218&near.do.colInfo=hprdP2p
>
>  We filtered out paths of length greater than two
>  because of exponential growth of lower-value interaction paths.
>
>  Our length 1 (and 0) paths should correspond to what you see
>  on the HPRD site, and the other (71 - 8 = 63) paths would probably
>  be interactions between those 8 and other proteins, for
>  a length of 2.  Without knowing the gene and assembly you
>  were looking at, this is just my speculation.
>
>  If you want more details about the exact construction
>  of our p2p paths, you would need to look at our make-docs.
>
>  We also have p2p interaction data from the E. Vidal and M. Wanker studies.
>
>  -Galt
>
>
>
>
>  On Fri, 11 Jan 2008, Edward Herman wrote:
>
>  > Hi,
>  > We have recently used the Gene Sorter tool on our gene of interest, and
>  > found a striking overlap between the list that this tool generated and our
>  > own data.  We would like to know more about what publications or results the
>  > Gene Sorter is based on and how we can access them.  In particular, we are
>  > interested in the HRPD Protein-Protein interaction database.  We tried their
>  > website (www.hprd.org) searching on our gene and clicking the "Interactions"
>  > tab, but only a subset (8 out of 71) appear here with links to publications.
>  >
>  > Can you tell us more about what data was used to generate the HRPD
>  > Protein-Protein interaction database on the Gene Sorter tool?
>  >
>  > Thanks,
>  > Eddie
>  > Geschwind Lab, UCLA
>
>
> > _______________________________________________
>  > Genome maillist  -  Genome at soe.ucsc.edu
>  > http://www.soe.ucsc.edu/mailman/listinfo/genome
>  >
>



-- 
Brett S. Abrahams, PhD
Program in Neurogenetics & Department of Neurology, UCLA
Room 2309, Gonda Neuroscience and Genetics Research Center
695 Charles Young Dr South, Los Angeles, CA 90095
Lab: (310) 794-7537 Cellular: (310) 347-9060
Fax: (866) 892-6444

http://myprofile.cos.com/abrahams
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