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Table 3 Results of the sign inference process on S. cerevisiae

From: Inferring the role of transcription factors in regulatory networks

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%
  1. 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.