[Genome] HPRD data in GeneSorter

[Galt Barber]

When I go to HPRD, I see pretty much the same list
of interactions there that we have, which is what
one would expect.

http://www.hprd.org/interactions?protein=01826&isoform_id=01826_1&isoform_name=

Name of Interactor  	   	Experiment Type  	   	Type
Nuclear transcription factor Y, beta 	In Vivo ; Yeast 2 Hybrid Direct
L1 cell adhesion molecule 	  	In Vitro 	  	Direct
Neurocan 	  	In Vitro 	  	Direct
Contactin associated protein like 2 	  	In Vitro 	 Direct
Contactin 1 	  	In Vitro 	  	Direct
NRCAM 	  	In Vitro 	  	Direct
Vac14 homolog 	  	In Vivo ; In Vitro ; Yeast 2 Hybrid 	  Direct

The only one that HPRD has that we don't have is Vac14 homolog,
and I think that it is because we don't have that in our knownGenes,
so GeneSorter has nothing to map to.

I got this by going to GeneSorter, choosing Human,
entering "uc001hbr.1" in the search,
going to configure columns, checking HPRD P2P to turn on the column,
and then back on the main view, selecting HPRD Protein-to-Protein
from the dropdown sort-by list.
I see the seven things you listed in your attachment,
exactly the same way.

I click the top link CNTN2 in the HPRD P2P column to go to HPRD site.
 http://www.hprd.org/protein/01826

I selected the "Interactions" tab.
If you read the genes, they look the same as in GeneSorter.
Does that answer your question?

The link you showed
> http://www.hprd.org/interactions?protein=15604&isoform_id=15604_1&isoform_name=

is Ubiquitin protein ligase E3C
which I don't think is associated with
Contactin 2 (uc001hbr.1) at all.

Hope that helps!

-Galt


On Sat, 12 Apr 2008, Brett Abrahams wrote:

> Hi Galt,
>
> 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
>