Pearson correlation vs. z-score.

<p>Gene pairs that are coregulated are represented by blue dots and those that are not coregulated are represented by red dots for <i>E. coli</i>.</p

F-score vs. z-score cutoff.

<p>F-score versus z-score cutoff for prediction of coregulated gene pairs and TRIs are plotted in blue and red respectively. Also, the F-score curves for the prediction of coregulated gene pairs in coexpression gene pairs with at least one TF gene is plotted in green. The five subplots correspond to the five established TRI data sets for <i>E. coli</i> and yeast (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031969#pone-0031969-t001" target="_blank">Table 1</a>), A) RegulonDB, B) Lee et al. 2002 (Chip-chip), C) Harbison et al. 2004 (Chip-chip/sequence motif), D) Milo et al. 2002 (Compilation) and E) Lee et al. 2002 (Compilation).</p

Mutual information vs. z-score for coregulated gene pairs in C and C-motifs.

<p>A) C and C-motifs. B–F) Data points for coregulated gene pairs in C and C-motifs are plotted in red and blue respectively. The five subplots correspond to the five established TRI data sets for <i>E. coli</i> and yeast (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031969#pone-0031969-t001" target="_blank">Table 1</a>), B) RegulonDB, C) Lee et al. 2002 (Chip-chip), D) Harbison et al. 2004 (Chip-chip/sequence motif), E) Milo et al. 2002 (Compilation) and F) Lee et al. 2002 (Compilation).</p

The number of TFs, regulated genes and edges in our established TRI data set of known TRIs for <i>E. coli</i> and yeast.

<p>The number of TFs, regulated genes and edges in our established TRI data set of known TRIs for <i>E. coli</i> and yeast.</p

Fractions of C-motifs in a group of subgraphs of coregulation vs. z-score cutoff on coregulated gene pairs in the group.

<p>A) C, C and C-motifs. B–F) The fractions of C, C and C-motifs are plotted in red, blue and green respectively. The five subplots correspond to the five established TRI data sets for <i>E. coli</i> and yeast (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031969#pone-0031969-t001" target="_blank">Table 1</a>), B) RegulonDB, C) Lee et al. 2002 (Chip-chip), D) Harbison et al. 2004 (Chip-chip/sequence motif), E) Milo et al. 2002 (Compilation) and F) Lee et al. 2002 (Compilation). G) C, C and C-motifs.</p

Fractions of MI-motifs vs. the z-score cutoff of non-interacting gene pairs.

<p>Non-interacting gene pairs in fan-out motifs are restricted to gene pairs with at least one TF gene. A) MI-motifs in which the non-interacting gene pair has the largest, intermediate and smallest MI. Fractions of MI, MI and MI- motifs are plotted in blue, red and green respectively for B) <i>E. coli</i> and C–F) yeast. The five subplots correspond to the five established TRI data sets for <i>E. coli</i> and yeast (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031969#pone-0031969-t001" target="_blank">Table 1</a>), B) RegulonDB, C) Lee et al. 2002 (Chip-chip), D) Harbison et al. 2004 (Chip-chip/sequence motif), E) Milo et al. 2002 (Compilation) and F) Lee et al. 2002 (Compilation).</p