Table 3

Results of the sign inference process on S. cerevisiae

Interaction network

Nodes

Edges

Average observed nodes

In/Out observed simultan.

Inferred signs {+, -}

MBM Type I

MBM Type II-IV

Total Inference

Naive Algorithm Inference


(A) Core of Transc. Network [11,28]

31

52

28%

88%

11

3

0

26.8%

11%

(B) Extended Transc. Network [11]

70

96

26%

72%

29

7

0

37.4%

15,6%

(C) MacIsaac inferred network [12,13]

83

131

33%

69%

21

4

0

19%

11%

(D) Global Transc. Network [11]

2419

4344

30%

52%

no filter : 631 filter k = 3 : 198

281

463

32%

13.9%


Sign inference process applied on four transcriptional networks of S. cerevisiae. 15 significant (2-fold) experiments were used for the inference. The In/Out observed simultaneously rate refers to the possible sign inference rate if all observations of the in/out nodes of one edge lead to predictions. The Inferred signs are the number of signs fixed in an unique way {+, -} by all the experiments; MBM Type I, refers to the number of edges found in a module of this type; and analogusly for MBM Type II-IV. The sum of these 3 values divided by the total number of edges will represent the rate of the Total Inference. In addition, we calculated the inference rate obtained with the Naive Algorithm. For network (D) all the inference rates were obtained using the algorithm without filtering, except for the number of Inferred signs.

Veber et al. BMC Bioinformatics 2008 9:228   doi:10.1186/1471-2105-9-228

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