Same protein list represented differently is web based string or string app in Cytoscape

[mzpet...@gmail.com]

Hi, I would like to represent 366 proteins obtained though proteomics as functional network. I have originally done it using string web software. However when I import the same list in Cytoscape and represent it with string app it looks different (denser, more connected; but have only string network uploaded, and no additional networks in the Cytoscape) even with same high confidence defined. No additional nodes or interactors were added in the Cytoscape representation. Obviously there are additional parameters I have not adjusted/verified. Looking into string app settings does not solves the problem. Any suggestions of settings I could look at?

[Scooter Morris]

Hi Maja,

   What version of the stringApp are you using?  There was a slight difference in the way the score was calculated between the stringApp and the string web site.  That was fixed in 1.4.1.  Give that a try -- you should now see the same edge count.

-- scooter