Table 2. Three-protein network motifs in the stringent network.

		No. of occurrences
		Stringent network			Nonstringent network			Comments regarding occurrences in the stringent network
Motif*	Illustration†	N real	N rand ± SD	z score	N real	N rand ± SD	Z score
A. Protein clique		1,293	14 ± 3.8	332.7	2,016	87 ± 10.8	177.9	1,198 occurrences in experimentally identified complexes
B. Interacting transcription factors that coregulate a third gene		243	2.4 ± 2.1	115.9	476	9.6 ± 7.8	59.7	21 pairs of coregulating proteins, most of which act in concert
C. Feed-forward loop		83	26 ± 6	9.5	994	473 ± 36.7	14.2	Analyzed in refs. 11, 40, and 41
D. Coregulated interacting proteins		66	2 ± 1.4	46.5	285	107 ± 10.1	17.7	25 sets of coregulated interacting proteins, most of which act in concert or participate in a common complex
E. Mixed-feedback loop between transcription factors that coregulate a gene		46	2.7 ± 1.6	26.3	118	8.2 ± 5.4	20.3	Four distinct pairs of transcription factors that are also involved in a mixed-feedback loop

^*These motifs were highly statistically significant in both the stringent and nonstringent networks; in all 1,000 randomized networks the number of their occurrences was lower than in the actual network.

^†A node represents a gene and its protein product; a red, directed edge represents a TRI; a black, bidirected edge represents a PPI.