On the origin of distribution patterns of motifs in biological networks

BMC Systems Biology

Table 1 Frequencies of canonical subgraph patterns in biological networks

	FFL	3-CYC	SIM	MIM	Bifan
(a) Yeast transcription – composite
n	997	4	107	1551	186
μ	993.5	4.2	76.8	1919.2	413.6
σ	281.4	2.4	27.0	233.1	111.1
z	0.0123	-0.0977	0.6734	-1.5792	-2.0479
(b) Yeast transcription – Cell Cycle
n	103	3	27	56	15
μ	79.3	1.9	28.0	76.6	31.7
σ	22.6	1.3	6.9	11.3	7.2
z	1.0491	0.9133	-0.1397	-1.8144	-2.3325
(c) Yeast transcription – Sporulation
n	67	2	27	41	26
μ	38.0	0.6	30.7	53.0	28.8
σ	12.5	0.8	5.1	7.8	7.8
z	2.3148	1.7739	-0.7303	-1.5336	-0.3544
(d) Yeast transcription – Diauxic Shift
n	64	1	48	137	54
μ	63.2	0.3	47.8	141.1	64.4
σ	27.2	0.6	13.7	18.2	16.6
z	0.0301	1.0626	0.0167	-0.2230	-0.6260
(e) Yeast transcription – DNA Damage
n	70	1	45	117	51
μ	49.0	0.2	44.9	117.1	53.4
σ	25.8	0.5	12.1	17.0	14.4
z	0.8149	1.6548	0.0076	-0.0073	-0.1679
(f) Yeast transcription – Stress Response
n	42	2	32	46	21
μ	36.1	0.3	40.5	52.7	24.0
σ	14.2	0.7	9.3	11.7	6.3
z	0.4123	2.4005	-0.9102	-0.5698	-0.4761
(g) *Escherichia coli* transcription
n	40	0	2	45	17
μ	24.1	0.4	4.7	29.0	17.5
σ	12.3	0.7	2.8	9.7	5.5
z	1.2928	-0.6379	-0.9663	1.6463	-0.1001
(h) Hippocampal CA1 neuronal signalling pathway
n	266	37	5	240	92
μ	219.3	21.7	4.6	181.1	103.7
σ	54.9	6.2	2.1	35.5	14.7
z	0.8499	2.4664	0.1994	1.6590	0.7992

Frequencies of FFL, 3-CYC, SIM, MIM, and Bifan in (a-f) various transcription networks of Saccharomyces cerevisiae, (g) transcription network of Escherichia coli, and (h) signalling pathway of hippocampal CA1 neuron. The observed frequencies, n, of these patterns in each of the networks were compared with the corresponding mean frequency (μ) in 1000 random networks having same degree sequences. The standard deviation (σ), and z-score $(z = \frac{n - μ}{σ})$ show the statistical relevance of various patterns. Positive and negative values of z signify the extent of over- and under-representation respectively, of n from μ (in σ units).

ISSN: 1752-0509