Integrating external biological knowledge in the construction of regulatory networks from time-series expression data

Table 4 Comparison of iBMA-prior, iBMA-shortlist and Lirnet in network construction on the Brem data

Method	Network size	p-value of chi square test^a	TPR (%)^b	# misclass.^c	TP	O/E^d
iBMA-prior	8000	7.75E-65	15.62	10198	323	2.41
iBMA-shortlist	35995	1.02E-59	10.99	14581	818	1.70
Lirnet	10491	1.90E-03	8.42	10080	132	1.30

^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.

ISSN: 1752-0509