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Table 4 Comparison with previous approaches based on gene expression response to TF deletion

From: Clustering of genes into regulons using integrated modeling-COGRIM

Method YAP1 SWI5 SWI4 GCN4
COGRIM (B+/C+) 7.24 × e-03 3.71 × e-04 1.23 × e-07 2.57 × e-11
COGRIM (B-/C+) 6.31 × e-03 1.01 × e-03 3.29 × e-03 4.40 × e-03
Model I (B+/C+) 0.018 4.00 × e-04 7.31 × e-04 4.80 × e-09
Model I (B-/C+) 0.012 8.14 × e-03 1.07 × e-03 7.95 × e-03
MA-Networker 0.021 1.81 × e-04 2.34 × e-06 2.17 × e-10
GRAM 0.259 0.281 1.14 × e-05 1.54 × e-04
ReMoDiscovery 0.102 7.73 × e-03 0.364 3.23 × e-10
ChIP binding data alone (B+) 0.194 0.036 9.80 × e-04 1.96 × e-04
  1. Standard t-tests were conducted to indicate the significance of the change in expression between knockout and wild-type. Model I, COGRIM without interaction terms; TF, transcription factor.