Evidence for the additions of clustered interacting nodes during the evolution of protein interaction networks from network motifs

Table 3 Constraints of functions on the co-origins of motif constituents

Functional Category ^a	The total number	Age homogeneity rate (%) ^c		Empirical P-value ^b	Age homogeneity ratio ^c
		Real network	Average of 1000 random networks
3-motif
Metabolism	3201	14.53	10.15	0.044	1.43
Energy	270	10.00	10.25	0.436	0.98
Cell cycle	5594	21.15	10.11	<10 ^-3	2.09
Transcription	6784	33.89	10.04	<10 ^-3	3.37
Protein synthesis	305	34.43	10.32	0.001	3.34
protein fate	7173	37.82	10.19	<10 ^-3	3.71
Binding protein	4755	26.71	10.14	<10 ^-3	2.63
Regulation of metabolism	96	25.00	10.23	0.021	2.44
Cellular transport	6811	29.14	10.11	<10 ^-3	2.88
Signal transduction	399	14.29	10.32	0.137	1.38
Cell defense	571	18.91	10.15	0.008	1.86
environment interaction	759	16.34	10.16	0.033	1.61
Cell fate	1505	19.73	10.12	0.003	1.95
Cellular components	3521	21.02	10.10	<10 ^-3	2.08
Cell differentiation	2378	18.84	10.10	0.002	1.87
4-motif
Metabolism	22981	5.07	3.75	0.178	1.35
Energy	949	1.79	3.65	0.641	0.49
Cell cycle	57466	8.57	3.61	0.019	2.37
Transcription	53928	24.05	3.66	<10 ^-3	6.58
Protein synthesis	765	18.95	3.64	0.002	5.21
protein fate	61470	29.36	3.66	<10 ^-3	8.02
Binding protein	29905	17.69	3.64	<10 ^-3	4.86
Regulation of metabolism	142	14.79	3.85	0.025	3.84
Cellular transport	61230	17.93	3.64	<10 ^-3	4.93
Signal transduction	1397	5.01	3.69	0.238	1.36
Cell defense	1889	8.31	3.72	0.038	2.23
environment interaction	2486	6.60	3.80	0.091	1.74
Cell fate	9484	8.31	3.65	0.016	2.28
Cellular components	24647	9.39	3.59	0.001	2.62
Cell differentiation	17140	8.05	3.61	0.007	2.23

^a Protein functional categories are based on FunCat functional classification system [49]. Here we list their abbreviations and please refer to Table S12 in additional file 1 for the details. ^b We list upper-tailed empirical P -values (enrichment), which are lower than 0.05 are highlighted in bold. ^c Please refer to the footnotes of Table 2 for the definitions of age homogeneity rate and age homogeneity ratio.

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