Summarizing cellular responses as biological process networks

BMC Systems Biology

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

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

“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.

ISSN: 1752-0509