Question: How to get PINs of Cancer and Normal
0
gravatar for Saeed Rahmani
3.0 years ago by
Iran/Zanjan/University of Zanjan
Saeed Rahmani10 wrote:

I need PINs data of Cancer and Normal tissue, I read this paper, and this paper say "we construct PINs from Cytoscape plugin". I want PINs data of Cancer and Normal tissue.

How to get or make PPI of gene expression or another way ?

ADD COMMENTlink modified 3.0 years ago by Jean-Karim Heriche18k • written 3.0 years ago by Saeed Rahmani10
2
gravatar for Shicheng Guo
3.0 years ago by
Shicheng Guo7.5k
Shicheng Guo7.5k wrote:

I know what's your meaning. However, there should be only few nodes or edge is cancer specific, therefore, the PIN from string 9.0 or cytoscape should be similar with cancer and normal network. in summary, you don't have cancer vs normal special network. the PIN in same species should be quite similar, even in, different kind of cell types. Finally, of course, if you can cancer and normal PIN data (array, NGS), you can build PIN by yourself.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Shicheng Guo7.5k

Thank you. I am a computer student, I know very small of biology. Can you help me in my project as fellow (or co-worker) ?

I have analyze Protein-Protein interaction of network of Cancer and normal tissue with graph theory, I am comparing parameters and review of graph.

I have greatest problem in finding data, that question of you.

ADD REPLYlink written 3.0 years ago by Saeed Rahmani10
1
gravatar for Jean-Karim Heriche
3.0 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

I don't know of any study that did a comprehensive proteomics analysis of tumor cells vs normal cells. As far as I know most studies infer protein interaction networks of cancer cells from gene expression profiles. This seems to be the approach taken by the paper you referenced (first sentence of the method section). Also consider that protein interaction databases of have a strong bias towards cancer proteins, e.g. oncogenes and other cancer-related genes have a higher degree (more interactions) than non-cancer proteins simply because they have been more studied, not because of any special biological property.

ADD COMMENTlink written 3.0 years ago by Jean-Karim Heriche18k

Do you have any cancer PPI to send me?

ADD REPLYlink written 3.0 years ago by Saeed Rahmani10
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