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Table 3 Statistics on BPLNs computed for the CS vs. HM contrast

From: Summarizing cellular responses as biological process networks

Link
significance
threshold
Processes Links Explained
perturbed
interactions
Unexplained
perturbed
interactions
CS vs. HM  
0.0001 191 1049 3186 675
1.51 ×10−25 23 20 698 3163
MCMC-BPN 27.6 20.0 1686.0 2175.0
Cirrhosis  
0.0001 99 199 994 960
9.04 ×10−14 15 14 176 1778
MCMC-BPN 18.0 14.0 380.0 1574.0
Very Advanced HCC  
0.0001 307 7249 13213 2187
2.26 ×10−81 27 38 2776 12624
MCMC-BPN 44.0 36.7 5670.7 9729.3
  1. “Link significance threshold” indicates the threshold value for which a link’s Benjamini-Hochberg-corrected p-value must be less than or equal to in order to declare the link significant. “Processes” indicates the number of processes involved in the BPLN and “links” the number of significant links between those processes. “Explained perturbed interactions” indicates the number of perturbed interactions explained by the links in the BPLN. “Unexplained perturbed interactions” indicates the number of perturbed interactions that are not explained by any link in the BPLN.