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Re: Computers may predict drugs’ side effects

From: David Wild <djwild@indiana.edu>
Date: Tue, 12 Jun 2012 13:46:46 -0400
Message-ID: <CANbBT=jq7i4bpY=p4UY1tYnynDmJYYH3K-VzSypJghdfXFgPEw@mail.gmail.com>
To: Oliver Ruebenacker <curoli@gmail.com>
Cc: "Lin MD, Simon" <LINMD.SIMON@mcrf.mfldclin.edu>, Joanne Luciano <jluciano@gmail.com>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>
So the subgraph doesn't show *all* paths between the compound and target -
just those that meet a level of statistical significance relative to
background distributions of path patterns in the dataset (the significance
level is tweakable in one of the boxes on the graph). Enclosed is a paper
preprint which explains this a bit better!

Also with the tool you can just enter either a compound or a target and
"virtual screen" targets/compounds to see the most related

Thanks for giving it a try!

David
____________________________________________________

Dr. David J. Wild, djwild@indiana.edu, http://djwild.info @davidjohnwild
Assistant Professor of Informatics & Computing
Director, Cheminformatics & Chemogenomics Research Group
Indiana University School of Informatics and Computing
901 E 10th St Rm 207, Bloomington, IN 47408
Tel. +1 812 856 1848



On Tue, Jun 12, 2012 at 1:10 PM, Oliver Ruebenacker <curoli@gmail.com>wrote:

>     Hello David,
>
> On Tue, Jun 12, 2012 at 12:58 PM, David Wild <djwild@indiana.edu> wrote:
> > Here it is -- bad name lookup on our part for sulfuric acid - using CID
> > instead 1118
> >
> >
> http://cheminfov.informatics.indiana.edu:8080/slap/slap.jsp?cid=1118&gene=Insulin
> >
> > Note the direct relationship is removed in the subgraph / calculation to
> > show indirect prediction.
>
>   Wouldn't you expect a bigger graph for a molecule that interacts
> with many targets?
>
>     Take care
>     Oliver
>
> --
> Oliver Ruebenacker
> Bioinformatics Consultant (
> http://www.knowomics.com/wiki/Oliver_Ruebenacker)
> Knowomics, The Bioinformatics Network (http://www.knowomics.com)
> SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)
>


Received on Tuesday, 12 June 2012 17:47:21 GMT

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