Experimentally, we performed STM algorithm on the yeast PPI data set using various merge threshold values to find the best threshold value for each data set. Experiments using 0.5,1.0,1.5, 2.0, 2.5, and 3.0 as the merge threshold were performed on each data set. The results show that when the merge threshold is less than 1.0, clusters that do not have substantial similarity are merged; and when the merge threshold is greater that 1.5, merging seldom occurred. There is no much performance difference when the values between 1.0 and 1.5 are used. The experiment when 1.0 is used as the merge threshold showed the best performance.