Question: How to get non-interacting protein pairs in Human
1
gravatar for lakshmi.bioinformatics
2.3 years 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 2.3 years ago • written 2.3 years ago by lakshmi.bioinformatics20
1
gravatar for Jean-Karim Heriche
2.3 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k 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 2.3 years ago by Jean-Karim Heriche21k
0
gravatar for lakshmi.bioinformatics
2.3 years 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 2.3 years 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 2.3 years ago by Jean-Karim Heriche21k

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 2.3 years ago by Jean-Karim Heriche21k
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