Question: How can I filter the list of targets protein in uniprotKB

[An_Ahmed]

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 via cytoscape 

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 

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 

[Scooter Morris]

Greetings,
    Alternative splicing certainly makes this difficult!  I would either query something like STRING with the gene names rather than going through the UniProt conversion, or just use the representative transcript for each of the genes.

-- scooter

[An_Ahmed]

Thanks for your reply Scooter

Could you be more specific Please? I am not pretty sure I understand your suggestion