Question: How to get non-interacting protein pairs in Human
1
gravatar for lakshmi.bioinformatics
4 months 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 4 months ago • written 4 months ago by lakshmi.bioinformatics20
1
gravatar for Jean-Karim Heriche
4 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche13k 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 4 months ago by Jean-Karim Heriche13k
0
gravatar for lakshmi.bioinformatics
4 months 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 4 months 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 4 months ago by Jean-Karim Heriche13k

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 4 months ago by Jean-Karim Heriche13k
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