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How to get PINs of Cancer and Normal

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 ?

protein pins network compelex cytoscape
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updated by Jean-Karim Heriche Jean-Karim Heriche • written by Saeed Rahmani • Saeed Rahmani

2 answers

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.

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written by Shicheng Guo Shicheng Guo

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.

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written by Saeed Rahmani • Saeed Rahmani

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.

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written by Jean-Karim Heriche Jean-Karim Heriche

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