I found a paper (https://www.nature.com/articles/s41556-018-0220-2#Fig5) that they created STRING protein-protein network and also gene ontology bar charts as in their Figure 5.
May I kindly ask you to let me have your valuable answers for my following questions please?
May I know how can I create the String network in such a way that it presents Direct binding of PtdIns(4,5)P2 in green nodes and Indirect PtdIns(4,5)P2 association in yellow nodes (as they did in their Figure 5)? Also, how they made some protein names with red text while the rest is black?
Also, I am highly interested to know how can I make gene ontology bar charts showing enriched terms along with -log10 (corrected P values) with red line, as they did.
I read STRING and DAVID databases but I could not find the options for making the above analyses and presentations. Any help to make these figures or similar ones with STRING, DAVID, or any other tools would be highly appreciated.
Many thanks. Best wishes,