Table 2
Summary of the assessment result for different network construction methods on the time-series gene expression data
Method Data used Network size p-value of chi sq testa TPR (%)b # mis-class.c TP O/Ed
iBMA-prior Gene expression + external data 21951 <1.00E-320 18.00 19282 593 4.11
iBMA-shortlist Gene expression + external data 67440 <1.00E-320 12.78 24673 1287 2.92
Network A from Yeung et al. Gene expression + external data 65122 1.68E-111 9.98 22485 662 2.28
LASSO-shortlist Gene expression + external data 255293 <1.00E-320 11.07 46482 4169 2.53
LAR-shortlist Gene expression + external data 242495 <1.00E-320 11.28 44765 4017 2.57
iBMA-size Gene expression data only 17202 5.75E-56 16.84 17622 114 3.84
iBMA-noprior Gene expression data only 63026 1.75E-23 8.85 18903 186 2.02
LASSO-noprior Gene expression data only 564321 2.56E-10 5.20 38399 1231 1.19
LAR-noprior Gene expression data only 194687 1.38E-40 7.71 22777 511 1.76

a The p-value of Pearson’s chi-square test measures the strength of association between an inferred network and the Yeastract database.

b True positive rate (TPR) is defined as the proportion of inferred regulatory relationships that are documented in Yeastract.

c The number of misclassified cases is the sum of false positives and false negatives.

d The O/E ratio is the number of folds the observed number of recovered relationships (i.e., TP) in excess of the expected count of recovery by chance.

Lo et al. BMC Systems Biology 2012 6:101   doi:10.1186/1752-0509-6-101

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