Comparing the GO enrichment of top 1000 human genes returned by the graph-based method and the score-only method. In the first plot, each point represents a cell cycle related GO category, and the X- and Y- axis represent the -(log p-value) in the score-only method and the graph-based method. Points above the diagonal line means the graph-based method assigns a lower p-value, i.e. more significance, to the GO category. It can be seen the graph-based method is superior to the score-only method.

Since the pvalues for a few GO categories are so close to zero, we show them in a second plot, comparing the enrichment by the counts (i.e. number of genes assigned to that category) instead of the p-values. Again, the graph-based method is superior.