Difference between string app and string database results

Question

[kumar.ajneesh]

Hello guys, I am using Cytoscape and I am importing the string results for the same input query from both string app and string database. But there is a difference between both string app and string database results for the same input query. I want to know why there is a difference between both results as both of them are the same? Thank you Kumar Ajneesh

Answer 1

[scooter]

Hi Ajneesh,

This typically has to do with the number of nodes you've requested and your cutoff value. For example, if you set a cutoff of 0.8 and you request 10 nodes, and there are 50 nodes with a score of 0.95, you will get 10 of those 50 nodes. The 10 you get from the stringApp might be slightly different than the 10 you get from the web site. Also, you should make sure that you are running the latest stringApp or you might be looking at an older database.

-- scooter

Answer 2

[damian.szk]

The network should indeed be identical.

Please confirm that: a) you are using the latest version of STRING (currently, v11.5), b) The network type is the same (full or physical), c) The combined score cut-off is the same, d) The evidence channels are all ticked.

All of the options you can change after you see the network in the "Settings" tab (on the webpage). With all of the above points adjusted you should get the exact same network (with slightly different layout).

Best,