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Table 3 The improvement in network modeling with the addition of prior knowledge

From: Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data

Data set Simulated data Yeast cell cycle study, benchmark from BIND Yeast cell cycle study, benchmark from ChIP-chip Mouse pancreas study
Number of genes 76 107 107 36
Number of established regulations 124 114 190 24
Number of possible regulations 76*75 = 5700 107*106/2 = 5671* 9*106 = 954 36*35 = 1260
Number of known regulations recovered with (without) prior knowledge 21 (14) 26 (13) 23 (11) 12 (6)
Total number of regulations predicted, with (without) prior knowledge 503 (440) 436 (387) 58 (33) 322 (297)
Improvement over plain BN χ 2 = 0.36,
p~0.54
χ 2 = 2.28, p < 0.13 χ 2 = 0.04, p~0.84 χ 2 = 0.98,
p~0.32
Improvement: over random selection χ 2 = 7.32,
p < 0.01
χ 2 = 24.5, p < 0.001 χ 2= 6.71, p < 0.01 χ 2 = 2.87,
p < 0.09
Plain BN over random
selection
χ 2 = 1.58,
p~0.2
χ 2 = 2.42, p~0.11 χ 2 = 1.6, p~0.2 χ 2 = 0.01, p~0.8
  1. * We ignored edge direction with comparing to BIND since it contains both directed and undirected interactions.