## Table 5 |
||||||

Assessment result for the different methods applied to data sets generated in the
stimulation study |
||||||

Method |
Data used |
Network size |
p-value of chi sq test^{a} |
TPR (%)^{b} |
# mis-class.^{c} |
TP |

iBMA-prior | Generated data + prior probability matrix | 14011 | <1.00E-320 | 71.13 | 16029 | 9966 |

iBMA-shortlist | Generated data + prior probability matrix | 30753 | <1.00E-320 | 47.23 | 23652 | 14526 |

iBMA-size | Generated data only | 9349 | <1.00E-320 | 20.31 | 27503 | 1899 |

iBMA-noprior | Generated data only | 29393 | <1.00E-320 | 8.55 | 46317 | 2513 |

^{a} The *p*-value of Pearson’s chi-square test measures the strength of association between an
inferred network and the true network for the simulation study.

^{b} True positive rate (TPR) is defined as the proportion of correctly inferred regulatory
relationships.

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

Remark: The values reported in the table were averaged across the 20 replications. The true network for the simulation study contained a total of 21951 edges.

Lo * et al.*

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