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Free Tool: Visualization of Gene Expression on Pathway

TOYODA Tetsuro toyop at gsc.riken.go.jp
Thu Jul 25 02:53:34 PDT 2002


Hi, Rama

I know "GenMapp" is a stand-alone application and its data file is a
relational database which you can open by using "Microsoft Access."

GSCope loads XML data file and is able to be used in web-browser,
VisualBasic etc., and has following functions,

Zooming and clipping of pathways
http://gscope.gsc.riken.go.jp/eng_manual/pathview.htm

Find similar expression profiles
http://gscope.gsc.riken.go.jp/eng_manual/findSimilar.htm

Cascade analysis
http://gscope.gsc.riken.go.jp/eng_manual/cascade.htm

Offers many programmable interfaces
http://gscope.gsc.riken.go.jp/eng_reference/SetResultXML.htm

You can see 417 Y2H PPI map as a whole view
http://gscope.gsc.riken.go.jp/sample_data/yeast_2hybrid/Y2H_sample.htm

Kind regards,
Tetsuro Toyoda


> -----Original Message-----
> From: owner-gofriends at genome.stanford.edu
> [mailto:owner-gofriends at genome.stanford.edu] On Behalf Of Rama
Balakrishnan
> Sent: Thursday, July 25, 2002 4:25 AM
> To: TOYODA Tetsuro
> Cc: gofriend at genome.Stanford.EDU
> Subject: Re: Free Tool: Visualization of Gene Expression on Pathway
> 
> Hi,
> 
> Are you familiar with  GenMapp?
> 
> http://www.genmapp.org/introduction.asp
> 
> They do something very similar.
> 
> Otherwise, it would be nice if you can make it compatible with MAC OS.
> 
> Thanks,
> 
> rama
> 
> On Wednesday, July 24, 2002, at 06:37 AM, TOYODA Tetsuro wrote:
> 
> > Dear colleagues,
> >
> > Let me introduce our visualization and analytical tools of gene
> > expression in the context of metabolic pathways.
> >
> > http://gscope.gsc.riken.go.jp/aboutGSCope.htm
> >
> > Two software packages are freely available at the web site.
> >
> > "GSCOPE" is a plug-in module for viewing complex biomolecular
> > connections. Data files for GSCOPE is XML-based. GSCOPE has many
> > functions including DNA microarray analysis, cascade deduction, find
by
> > keyword, etc.
> >
> > "Knowledge Editor" is a stand alone application, by which you can
draw
> > pathway data (XML) while analyzing DNA-microarray similarities.
> >
> > Currently, both programs works only on Windows2000 or WindowsXP with
> > Internet Explorer 5.5 or more.
> >
> > See samples at our web site.
> > http://gscope.gsc.riken.go.jp
> > 1) Metabolic pathways with mouse and yeast gene expression data.
> > 2) Orthologs estimated by our original analysis program ( not yet
> > published).
> > 3) Protein-Protein Interactions of 417 proteins found by yeast 2
hybrid.
> >
> >
> > Best regards,
> > Tetsuro Toyoda.
> >
> >
> > --
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> 
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