how to make a network using HPR database?
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5.1 years ago
Mo ▴ 920

I would like to know whether and how it is possible to make a network using

http://www.hprd.org/download

Lets say my protein list is as follows:

P41182, P56524, P41182, Q9UQL6, P41182, Q8WUI4, Q92793, Q09472, Q9Y6Q9, Q92831

is it also possible to use Cytoscape to make a interaction network for these proteins?

proteomics • 1.0k views
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Do you mean you want to extract the subgraph containing your proteins from the HPRD graph ? And if so, do you want only direct interactions ?

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@Jean-Karim Heriche can you please give different examples?

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You haven't clarified what you wanted. I am still unsure what you're after. Assuming you want to extract from HPRD only direct interactions between your proteins, you could do so by reading the HPRD file and extracting all the lines in which both interaction partners are in your list.

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@ean-Karim Heriche Lets say only getting direct interactions, is there any automatic way to do it ?

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Yes, write a script to do what I described above. By the way, the HPRD data hasn't been updated in about 6 years so I would use something more comprehensive and up-to-date like iRefindex.

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