New to Cytoscape, would like to use proteomic data

[Sarcoma]

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]

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%20Edge%20Attributes
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

--
Piet Molenaar
p.mol...@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

[Dariel Ashton-Beaucage]

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) 343-6111 ext.8092
d.ashton...@umontreal.ca

[Sarcoma]

Dear Piet:

Thanks for your reply.

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

I would like to map my data. Now, I have used GoMiner to identify
ontology categories that appear to be active.

Do you have an opinion as to if it would be best (i.e. easiest for a
newbie like me) to map genes or ontology categories?

best regards,

Tim

[Sarcoma]

Dear Dariel:

Very good, I'll go and take a look.

Thank you for these helpful suggestions,

Tim

On Jun 19, 1:16 pm, Dariel Ashton-Beaucage <darie...@gmail.com> wrote:
> 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