Re: [cytoscape-helpdesk] Re: Disease-protein network

[Diego Bonatto]

Dear researchers,

My research group developed a web server (BioNet) that allow to
collect the proteins associated with a specific disease from OMIM site
[http://www.ncbi.nlm.nih.gov/omim] and use these data to generate
protein-protein interaction network from the site STRING
[http://string.embl.de/]. The archives can be saved in different
formats to be used in Cytoscape.
Please feel free to make suggestions to improve the web server. BioNet
is still under construction and any suggestion is welcome. The link to
access BioNet is www.biosoft.bio.br
Regards,
Diego Bonatto

On Sat, Dec 5, 2009 at 12:05 AM, Majid <majid....@gmail.com> wrote:
> Interesting
> Thanks Russ, I am going to use it.
> Best,
> M
>
>
>
> On Dec 4, 7:04 am, Russ <russell.h...@liv.ac.uk> wrote:
>> Cool.
>> I thought Allan's method for filtering disease nodes a bit long-winded
>> to be honest.  Had I done this, I'd have introduced a node attribute
>> 'Disease' which would take the value 1 for all your disease nodes.
>> Selecting the disease nodes is then trivial using either the new or
>> old filters. Importantly, once the attribute is set up, you could also
>> alter the shape/colour of the disease nodes relative to the protein
>> nodes for improved visuals.
>>
>> Regards
>> Russ
>
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--
Dr. Diego Bonatto
Laboratorio de Genetica Toxicologica - 206
Instituto de Biotecnologia
Centro de Ciencias Biologicas e da Saude
Universidade de Caxias do Sul - UCS
Rua Francisco Getulio Vargas 1130 – Bloco 57
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BRAZIL
95070-560
Phone: 55-54-3218-2100 (Extension: 2682)
Fax: 55-54-3218-2293
Alternative e-mail: dbon...@ucs.br

[Cheng Luo]

When I use string.embl.de to test BNC1 and BNC2, quite a surprise, I
saw there are more than 10 genes linked, especially for BNC2. There is
always only 1 or 2 link in other gene network. I hope it is meaningful
to use this interaction network as guide for choosing the oligos for
qRT-PCR? Someone like to give some comments?

Thanks!

Cheng (Lu...@yahoo.com)

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