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 Math 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).

Konagurthu and Lesk BMC Systems Biology 2008 2:73   doi:10.1186/1752-0509-2-73