Figure 3. Network motifs in the yeast phosphorylation network.

(A) Three common motifs were enriched in the phosphorylation network: (1) a bi-fan motif in which two regulators bind common targets; (2) a bi-parallel motif in which one regulator controls two other regulators that in turn regulate one target gene; and (3) a single input module motif in which one regulator binds to multiple targets. (B) Seven three-element kinase-centered composite motifs are listed: (1) an interacting kinate motif in which one kinase phosphorylates two interacting substrates; (2) a scaffold motif in which one protein interacts with both a kinase and its substrate; (3) a TF-regulated kinate motif in which one TF regulates the expression of both a kinase and its substrate; (4) a kinate regulon motif in which one kinase phosphorylates both a TF and the target regulated by the TF; (5) a kinate feedback loop I motif in which a kinase phosphorylates a protein that interacts with a TF that in turn regulates the expression of that kinase; (6) a kinate feedback loop II motif in which a kinase phosphorylates a TF whose target physically interacts with the kinase; and (7) a heterosubstrate regulation motif in which an interacting kinase and TF regulate one target together. Motifs (1) – (5) were enriched in the yeast integrated network.

TF: Transcription factor.

The enrichment p-values in (A) are generated by mfinder [63].