Question: How to get non-interacting protein pairs in Human
1
gravatar for lakshmi.bioinformatics
7 days ago by
India
lakshmi.bioinformatics20 wrote:

I am working on human protein protein interaction I need to run SVM I need a negative data set comprising of non interacting protein pairs how to generate these. I found this database Negatome (http://mips.helmholtz-muenchen.de/proj/ppi/negatome/) but the the problem is it talking about most mammals I cant restrict my search to human. Is there any other database containing human non interacting protein pairs or is there any other method to do this. Thanks in advance.

ADD COMMENTlink modified 6 days ago • written 7 days ago by lakshmi.bioinformatics20
1
gravatar for Jean-Karim Heriche
6 days ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche11k wrote:

The Negatome database contain some human proteins which you can extract. In addition, there's this paper (and data here). Also if your protein interaction data is from AP-MS, you may want to make use of the CRAPome database.

ADD COMMENTlink written 6 days ago by Jean-Karim Heriche11k
0
gravatar for lakshmi.bioinformatics
6 days ago by
India
lakshmi.bioinformatics20 wrote:

Thank you @Jean-Karim Heriche

My data is from online databases and its not an experimental one thanks again for the information. How to extract only the human Ids from Negatome

ADD COMMENTlink written 6 days ago by lakshmi.bioinformatics20

As far as I remember, the Negatome database uses UniProt accession numbers so you could use UniProt's REST API to figure out which species each protein belongs to. If you want to combine data sets from multiple sources, I would suggest to map the different IDs to the same human reference genome annotation e.g. EnsEMBL.

ADD REPLYlink written 6 days ago by Jean-Karim Heriche11k

Use the "Add comment" button when replying to an answer. This keeps the discussion organized and doesn't mislead users by creating answers that are not real answers to the question.

ADD REPLYlink written 6 days ago by Jean-Karim Heriche11k
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