I have a list of interested differentially express genes. I integrated my gene with PPI network via using UniProt website http://www.uniprot.org. First, I convert Entrez Genes to UniProtKB then I download the list of targets protein. Then I used this list to get the PPI network.
In the list of targets proteins I have more than one protein for each gene such as:
UniProt Gene symbol Gene ID 'B4DNQ5' 'IL6' 3569 'B4DVM1' 'IL6' 3569 'B5MC21' 'IL6' 3569 'P05231' 'IL6' 3569 'Q75MH2' 'IL6' 3569
my question is that how can I deal with proteins that belong to one gene if I want to I score my target pathway according to gene P-value??
Any help will be highly appreciated