On Wed, Jun 17, 2009 at 4:37 PM, Sarcoma <chairsid...@yahoo.com> wrote:

> Hello everyone:

> I am comparing benign to malignant tumors using mass spec.  I have
> data from several patients for each group.  I've looked at the FAQ and
> tutorials.  It is unclear to me how best to prepare my data for use in
> cytoscape - can I make my own?  what about gene ontology associations?

> Sorry if these are incredibly naive questions.

> Thanks,

> Tim

On Fri, Jun 19, 2009 at 9:52 AM, piet molenaar <piet....@gmail.com> wrote:
> Hi Tim,
> The first thing to consider is what you actually want. Map your data onto
> networks or derive networks from your data? The first case might be a
> starting point. You can import known pathways and annotate these with your
> data. In that case I would advise you to study the manual:
> http://www.cytoscape.org/manual/Cytoscape2_6Manual.html and more
> specifically the attributes section
> http://www.cytoscape.org/manual/Cytoscape2_6Manual.html#Node%20and%20...
> Deriving networks is no standard procedure; in that case you should
> consider specific plugins but I think most of them are geared towards array
> data...
> Hope this helps for a start,
> Piet

> On Wed, Jun 17, 2009 at 4:37 PM, Sarcoma <chairsid...@yahoo.com> wrote:

>> Hello everyone:

>> I am comparing benign to malignant tumors using mass spec.  I have
>> data from several patients for each group.  I've looked at the FAQ and
>> tutorials.  It is unclear to me how best to prepare my data for use in
>> cytoscape - can I make my own?  what about gene ontology associations?

>> Sorry if these are incredibly naive questions.

>> Thanks,

>> Tim

> --
> Piet Molenaar
> p.molen...@amc.uva.nl
> Department of Human Genetics, M1-131
> Academic Medical Center
> University of Amsterdam
> Meibergdreef 9
> 1105 AZ Amsterdam
> the Netherlands

> tel (+31) 20-5666592
> fax (+31) 20-6918626

> The first thing to consider is what you actually want. Map your data onto
> networks or derive networks from your data?

> I'm not a Cytoscape expert, but to map data onto networks, one plugin I
> found particularly useful and easy to use is APID2NET (http://bioinfow.dep.usal.es/apid/apid2net.html). It might be a good one to
> try out first. BioNetBuilder (http://err.bio.nyu.edu/cytoscape/bionetbuilder/index.php) is another nice
> one. Maybe this might be useful in your case.
> cheers
> Dariel
> _____________________________
> Dariel Ashton-Beaucage
> IRIC - Université de Montréal(514) 343-6111ext.8092
> d.ashton-beauc...@umontreal.ca

> On Fri, Jun 19, 2009 at 9:52 AM, piet molenaar <piet....@gmail.com> wrote:
> > Hi Tim,
> > The first thing to consider is what you actually want. Map your data onto
> > networks or derive networks from your data? The first case might be a
> > starting point. You can import known pathways and annotate these with your
> > data. In that case I would advise you to study the manual:
> >http://www.cytoscape.org/manual/Cytoscape2_6Manual.htmland more
> > specifically the attributes section
> >http://www.cytoscape.org/manual/Cytoscape2_6Manual.html#Node%20and%20...
> > Deriving networks is no standard procedure; in that case you should
> > consider specific plugins but I think most of them are geared towards array
> > data...
> > Hope this helps for a start,
> > Piet

> > On Wed, Jun 17, 2009 at 4:37 PM, Sarcoma <chairsid...@yahoo.com> wrote:

> >> Hello everyone:

> >> I am comparing benign to malignant tumors using mass spec.  I have
> >> data from several patients for each group.  I've looked at the FAQ and
> >> tutorials.  It is unclear to me how best to prepare my data for use in
> >> cytoscape - can I make my own?  what about gene ontology associations?

> >> Sorry if these are incredibly naive questions.

> >> Thanks,

> >> Tim

> > --
> > Piet Molenaar
> > p.molen...@amc.uva.nl
> > Department of Human Genetics, M1-131
> > Academic Medical Center
> > University of Amsterdam
> > Meibergdreef 9
> > 1105 AZ Amsterdam
> > the Netherlands

> > tel (+31) 20-5666592
> > fax (+31) 20-6918626