Table 1. Tables of all 30 PPIN datasets analysed in this study.

No.	Name	Method	NP	NI	k_mean	k_max	kk_corr	ev	evc_mean	btwn	assort	transitivity	Loop3	Loop4	Loop5	Loop6	Reference
1	C.elegans I	Y2H	3512	6540	3.72	524	187.71	57.27	0.02	10623.78	−0.17	0.01941	2090	83280	752345	23946948	Simonis et al. 2008
2	C.elegans II	Y2H	2500	3706	2.96	99	40.93	26.66	0.03	8467.91	−0.17	0.01985	314	3296	14865	136047	Simonis et al. 2008
3	C.jejuni	Y2H	1324	11596	17.52	207	870.88	91.39	0.09	2514.98	−0.26	0.0847	15950	758928	16914130	654090932	Parrish et al. 2007
4	H.pylori	Y2H	724	1403	3.88	55	45.21	20.93	0.07	2191.72	−0.24	0.01524	76	1117	3135	31491	Rain et al. 2001
5	H.sapiens I	Y2H	1499	2529	3.37	125	63.56	30.52	0.03	3735.18	−0.2	0.01856	279	5961	20393	388133	Rual et al. 2005
6	H.sapiens II	Y2H	1655	3075	3.72	95	62.96	35.04	0.03	5665.36	−0.19	0.00612	100	15930	18031	1989139	Stelzl et al. 2005
7	H.sapiens VIII	Y2H	2163	3718	3.44	154	73.1	32.65	0.03	6053.26	−0.2	0.0143	359	8150	31332	624516	Yu et al. 2011
8	M.loti	Y2H	1803	3094	3.43	401	130.27	43.47	0.02	4907.73	−0.11	0.00467	178	9254	15670	549649	Shimoda et al. 2008
9	P.falciparum	Y2H	1267	2643	4.17	51	47.66	24.49	0.05	3897.5	−0.03	0.02515	231	1648	11617	89389	Lacount et al. 2005
10	S.cerevisiae I	Y2H	991	905	1.83	24	6.74	11.67	0.01	1477.63	−0.09	0.03569	29	97	132	287	Uetz et al. 2000
11	S.cerevisiae II	Y2H	787	754	1.92	55	12.11	16.16	0.02	1140.11	−0.11	0.02	33	203	127	653	Ito et al. 2001 (core)
12	S.cerevisiae III	Y2H	3241	4367	2.69	279	73.11	33.91	0.01	9410.27	−0.18	0.00478	182	2353	6512	75500	Ito et al. 2001
13	S.cerevisiae XII	Y2H	1544	1809	2.34	86	23.1	22.27	0.01	3645.2	−0.1	0	0	2268	0	48775	Yu et al. 2008
14	Synechocystis	Y2H	1903	3100	3.26	51	24.28	17.91	0.02	8042.43	−0.07	0.00705	47	722	1213	10606	Sato et al. 2007
15	T.pallidum	Y2H	724	3627	10.02	285	557.46	75.18	0.08	1412.82	−0.32	0.08837	5838	248720	4902417	165397982	Titz et al. 2008
16	E.coli	AP-MS	2457	8663	7.05	641	458.59	64.07	0.03	5692.11	−0.15	0.01667	3085	100359	1317533	33928580	Arifuzzaman et al. 2006
17	H.sapiens III	AP-MS	2268	6432	5.67	314	317.48	62.74	0.03	6351.31	−0.33	0.00724	854	162851	437160	63110028	Ewing et al. 2007
18	S.cerevisiae IV	AP-MS	1576	3616	4.59	62	68.01	27.71	0.06	4997.83	−0.22	0.03	508	6466	25872	338489	Ho et al. 2002
19	S.cerevisiae VI	AP-MS	1359	3220	4.74	53	57.2	28.69	0.03	4432.92	−0.12	0.19	2300	18289	109032	877046	Gavin et al. 2002
20	S.cerevisiae VIII	AP-MS	2551	21393	16.77	955	1816.57	133.44	0.04	4613.46	−0.18	0.06541	50054	3184108	87841860	1778224626	Gavin et al. 2006
21	S.cerevisiae IX	AP-MS	2708	7121	5.26	141	84.44	38.29	0.03	9052.32	−0.01	0.19489	6965	58733	524036	5346961	Krogan et al. 2006
22	S.cerevisiae X	AP-MS	1630	9089	11.15	127	387.19	119.85	0.04	2966.71	0.61	0.61741	63073	1956777	77162029	3399697999	Collins et al. 2007
23	H.sapiens V	BP-MS	2630	12104	9.2	165	296.47	117.18	0.03	8081.47	0.43	0.38	47270	1628074	66164738	2909934167	Havugimana et al. 2012
24	S.cerevisiae XI	PCA	1078	2804	4.7	58	74.55	46.95	0.03	3367.52	0.18	0.28215	3541	43225	594537	9092371	Tarassov et al. 2008
25	D.melanogaster	DD	7278	24930	6.85	176	159.53	51.61	0.03	23502.06	−0.03	0.02732	5060	127024	1045293	26171738	Stark et al. 2006
26	H.sapiens IV	DD	9306	35021	7.53	247	252.86	75.13	0.02	28722.66	−0.05	0.05315	20227	392393	7261987	188377492	Prasad et al. 2009
27	S.cerevisiae V	DI	2617	11855	9.06	118	306.04	131.51	0.03	8824.76	0.46	0.46862	60701	2651679	114266735	1657681843	Von Mering et al. 2002
28	S.cerevisiae VII	DI	1379	2493	3.62	32	30.63	40.78	0.02	3707.17	0.44	0.54	3371	31747	329752	4113240	Han et al. 2005
29	H.sapiens VI	DD	2590	4509	3.48	102	43.62	54.11	0.01	919.8	0.31	0.26	4522	66869	1091253	21251342	Lu et al. 2013
30	H.sapiens VII	DD	2623	4292	3.27	90	41.37	37.11	0.01	5698.33	0.02	0.09844	1640	39702	166070	5040903	Meyer et al. 2013

The datasets cover a range of source organisms and a variety of experimental techniques (Methods). The names of datasets, their detection methods and references are presented along with properties of each network. The number of proteins (NP) and interactions (NI) for each network are reported in this table alongside a selected set of global topological properties of the network: measures of connectivity such as the average (k_mean) and maximum degree (k_max), indices of node centrality such as the average betweenness (btwn), the average eigenvector centrality (evc_mean) and the first eigenvalue of the graph adjacent matrix (ev), as well as measures of the relationship between nodes such as the assortativity coefficient (assort)⁴², the transitivity ratio (transitivity)²⁹ and the average degree-degree correlation (kk_corr)²⁰,²⁷. Values were calculated using R igraph package⁴³ and in-house developed code²⁰.