You can see CytoScape software to accomplish your work.

Dear Jade Davies

You can use DAVID to convert UniProt IDs to gene names, or even the Uniprot system does it for you. And so, use the Enrichr!

Often it is not necessary to convert the gene name to do it. For this, you can use PANTHER or DAVID to do the functional enrichment analysis by looking for molecular function, cellular component and biological process (with UniProt ID).

DAVID = https://david.ncifcrf.gov/

PANTHER = http://www.pantherdb.org/

Best,

Leite

You can also use the simple program STRAP. By providing a list of UniProtKB accession numbers, STRAP will download the GO information directly from UniProtKB allowing you to compare the two conditions. Link:

http://www.bumc.bu.edu/msr/software/strap/

There is also a free online database called DAVID you could use. It has a feature to convert accession number into gene ID.

Dear Jade Davies,

As par your interest, you can collect the Gene Ontology ID from the respective UniProt ID and to predict the logP value by David/ Panther/ GO consortium/BiNGO/Gorilla servers-based on organisms.

After, remove the redundant entries of GO and make the list of GO with P-values submit to REVIGO server (http://revigo.irb.hr/) according to mentioned algorithm. Then the result output linked to Cytoscape plugin and furnish the differential protein network based on molecular function.

As well as you can try to VENN analysis for the classification of GO entries by protein functions and location.

Kindly check this article GO analysis:

Muthukumar, S., Rajkumar, R., Rajesh, D., Saibaba, G., Liao, C. C., Archunan, G., ... & Gulyas, B. (2014). Exploration of salivary proteins in buffalo: an approach to find marker proteins for estrus. The FASEB Journal, 28(11), 4700-4709.

Article Exploration of salivary proteins in buffalo: An approach to ...

Hope it is useful.

Regards,

Rajesh