Supplementary Table 1.

The p-values and the rankings of the top 10 affected pathways of four datasets using top-down approach. Among these pathways, 5 pathways (shown in bold) are commonly overrepresented for the dysregulated modules of T2D1, T2D2, T2D3, T2DC datasets.

	p-values				Rank				# of genes identified in different datasets (DD)				# of genes found in at least one dataset (Union)	# of genes in pathway (GiP)	Percent of identified genes in pathways
															max (DD) / GiP	Union / GiP
KEGG term	T2DC	T2D1	T2D2	T2D3	T2DC	T2D1	T2D2	T2D3	T2DC	T2D1	T2D2	T2D3
Spliceosome	8.55E-39	3.26E-27	6.95E-30	3.10E-41	1	15	8	5	65	62	75	85	104	127	0.66	0.81
Focal adhesion	7.032E-38	1.80E-30	3.82E-42	1.97E-54	2	10	1	1	150	135	146	146	172	200	0.75	0.86
SNARE interactions in vesicular transport	1.98E-35	1.37E-37	8.16E-33	5.41E-44	3	3	5	4	31	30	29	32	34	36	0.88	0.94
Valine leucine and isoleucine degradation	5.97E-35	3.26E-43	6.39E-20	3.34E-29	4	1	34	13	36	36	35	37	41	44	0.84	0.93
Purine metabolism	7.60E-34	5.35E-43	4.92E-12	1.29E-45	5	2	83	3	54	57	34	92	99	166	0.55	0.59
Dopaminergic synapse	3.26E-33	1.04E-20	9.48E-32	6.80E-34	6	37	7	9	107	107	110	103	119	130	0.84	0.91
TGF-beta signaling pathway	5.03E-29	8.70E-32	5.61E-34	3.23E-28	7	6	3	15	62	64	64	58	75	84	0.76	0.89
ErbB signaling pathway	1.59E-28	4.64E-31	1.00E-29	1.46E-37	8	8	9	7	84	80	82	81	85	87	0.96	0.97
Chemokine signaling pathway	5.23E-28	1.47E-21	1.01E-23	2.97E-19	9	33	20	39	107	139	111	129	163	189	0.73	0.86
Glutamatergic synapse	3.47E-27	1.97E-20	1.94E-29	3.03E-28	10	38	10	14	81	86	88	87	101	126	0.69	0.80