[Genome] GeneSorter References

[Edward Herman]

Thanks, this helps a lot.  I guess at first we didn't notice the "HPRD P2P"
column,, but now I see that it lists not only the direct protein interactors
but the interactors-of-interactors as well.  We are reminded of the Kevin
Bacon Effect, and I wonder if you didn't include path length of 3 because
its the whole genome...

Thanks again,
Eddie

On Jan 11, 2008 4:03 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
> >
>