Interpreting plots from Cytoscape

Question

[xmsterl]

I am trying to analyze a gene network using Cytoscape. To do this, I used the 'Node degree distribution' and 'Betweenness by degree' functions from the analyzer tool. Both these functions generate a plot. However, I'm having a hard time interpreting these plots. The top plot is Betweenness by degree, the bottom is Node degree distribution. I don't understand what the axes in both plots mean. What do 'stringdb::score' and 'stringdb::textmining' stand for, and what do the numbers on the y-axis of the Node degree distribution plot represent?

Answer 1

[scooter]

Hi there,

As near as I can tell, the first plot is actually a plot of the string score vs. the string textmining score (I assume you created your network using the stringApp?). The plot does make sense in that context as it looks like you used 0.4 as your cutoff. As far as interpreting a plot of the string textmining score vs. overall score, I'm not sure it's really useful. I'm not sure what the second plot is -- It looks like string score vs. something else -- certainly not degree since a degree distribution would have integer values.

-- scooter