# Table 1 Link-specific ChIP evaluation bootstrap results

Predicting regulation by single TFs
Top 50 Top 100 Top 200
P32 P2 ML Inf   P32 P2 ML Inf   P32 P2 ML Inf
P32    *** * P32    ** ** P32    ** **
P2    *** ** P2 +   *** *** P2    *** **
ML      ML      ML
Inf      Inf      Inf
Top 400 Top 800 Top 1600
P32 P2 ML Inf   P32 P2 ML Inf   P32 P2 ML Inf
P32    * *** P32    + *** P32    * ***
P2    ** *** P2    * *** P2    * ***
ML     * ML     *** ML     ***
Inf      Inf      Inf
Top 3200
P32 P2 ML Inf
P32   *** *** ***
P2    * ***
ML     ***
Inf
Predicting regulation by TF pairs
Top 50 Top 100 Top 200
P32 P4 ML Inf   P32 P4 ML Inf   P32 P4 ML Inf
P32    ** + P32    * . P32    + *
P4    ** + P4    * + P4    + *
ML      ML      ML
Inf    .   Inf      Inf
Top 400 Top 800 Top 1600
P32 P4 ML Inf   P32 P4 ML Inf   P32 P4 ML Inf
P32    * ** P32    + *** P32     **
P4    + ** P4    * *** P4 **   * ***
ML      ML     . ML     +
Inf      Inf      Inf
Top 3200
P32 P4 ML Inf
P32     *
P4 ***   ** ***
ML *    ***
Inf
1. The results of 100,000-fold bootstrap resampling of the data set of observed genes to assess significance of differences in ranking method performance. The methods studied are: P32 = Posterior-32 method, P2 = Posterior-2 method, P4 = Posterior-4 method, ML = ML Baseline method, Inf = Inferelator. For each pair of methods, the marks in the tables show how often the method on the corresponding row dominated the one on the corresponding column. The marks are interpreted as follows: ‘.’: >80% dominance, ‘+’: >90% dominance, ‘*’: > 95% dominance, ‘**’: >99% dominance, ‘***’: >99.9% dominance, ‘-’: comparison not applicable.