search

jdrudolph / photon

PHOsphoproteomic dissecTiOn using Networks
GNU General Public License v3.0
17 stars 5 forks source link

Phosphosite information #10

Closed Spacebio closed 7 years ago

Spacebio commented 7 years ago

Hi,

I have a question about your tool, how did you store and use the phosphosite information?

Thanks! Corinne

jdrudolph commented 7 years ago

could you be more specific about which information you mean?

Spacebio commented 7 years ago

I meant, how did you link the phosphosite data to the PPI network to map it? Where can I find this script? and is it possible to to use symbols ot entities rather than entrez ID?

Thank you, C.

jdrudolph commented 7 years ago

You have to make some compromise between the network and the data. I chose to map the data from uniprot to the entrez gene ids used for the network. If I were to map it the other way round, my network would be cluttered with duplicated entries stemming from the (one gene id) => (many uniprot ids) mapping.

I don't know for sure how it'll work out but if the identifiers are consistent between the network and the data you should be able to run the functionality score and network reconstruction from the command line. In order for the full pipeline to work you will need to provide a custom idmapping file instead of db/uniprot/HUMAN_9606_idmapping.dat.gz which will allow the curated site information from phosphosite plus to be mapped to your custom identifiers.

If you want to map your own data from uniprot to entrez you could use the code in util/mapping.py