Table 4. P-values, direction and connectivity of genes that consist of significant gene sets and satisfied p < 0.05 in the Affymetrix and Illumina platforms.

P-values and direction were obtained using the “Globaltest” R package. An up or down direction indicates that the expression of a gene is up- or down-regulated in sphere cells, respectively. Connectivity, scaled connectivity and clustering coefficients were obtained from WGCNA for each gene set.

Gene Sets	Genes	Affymetrix					Illumina
		p-value	Direction	Connectivity	Scaled Connectivity	Clustering Coefficient	p-value	direction	Connectivity	Scaled Connectivity	Clustering Coefficient
Cytokine-cytokine receptor interaction	CXCL10	0.004	Down	7.339	0.484	0.217	0.038	up	58.222	0.932	0.460
	CXCL6	0.009	Down	4.709	0.311	0.139	0.028	up	57.983	0.928	0.459
	IL12RB2	0.013	Up	1.703	0.112	0.053	0.030	up	57.588	0.922	0.475
	CXCL1	0.014	up	2.619	0.173	0.082	0.011	up	60.767	0.972	0.475
	TNFRSF11B	0.022	down	1.641	0.108	0.040	0.009	up	61.191	0.979	0.478
	CXCR4	0.029	up	1.486	0.098	0.108	0.001	up	62.369	0.998	0.483
Valine, leucine and isoleucine degradation	PCCB	0.000	up	0.156	0.023	0.088	0.025	down	13.050	0.630	0.531
	ACADM	0.004	up	1.076	0.162	0.091	0.013	up	14.366	0.693	0.519
	BCKDHB	0.015	up	3.931	0.591	0.187	0.037	up	16.723	0.807	0.560
	AOX1	0.036	down	3.608	0.543	0.251	0.023	up	14.370	0.694	0.551
	HMGCS1	0.038	up	6.083	0.915	0.261	0.005	up	16.723	0.807	0.495
Systemic lupus erythematosus	HIST1H2BD	0.000	down	6.428	1.000	0.297	0.037	up	34.910	0.862	0.491
	HLA-DMA	0.001	up	1.531	0.238	0.209	0.049	up	34.737	0.858	0.501
	HIST2H3A	0.002	down	6.424	0.999	0.332	0.004	up	16.371	0.404	0.376
	HIST1H2BC	0.006	down	5.389	0.838	0.329	0.018	up	38.786	0.958	0.523
	H2AFJ	0.013	down	5.692	0.886	0.364	0.008	up	40.420	0.999	0.533
	SSB	0.026	up	1.982	0.308	0.092	0.025	down	37.591	0.929	0.514
	HIST2H2BE	0.045	down	6.190	0.963	0.314	0.000	up	39.830	0.984	0.529
DNA replication	RfC4	0.000	up	2.324	0.435	0.142	0.030	down	19.755	0.917	0.603
	RPA1	0.002	up	4.078	0.763	0.207	0.001	down	21.553	1.000	0.626
	MCM4	0.005	up	2.725	0.510	0.274	0.001	down	21.239	0.985	0.639
	MCM5	0.007	up	2.773	0.519	0.301	0.014	down	19.233	0.892	0.643
	MCM2	0.009	up	3.880	0.726	0.201	0.009	down	19.912	0.924	0.638
	FEN1	0.022	up	3.304	0.618	0.209	0.039	down	18.427	0.855	0.650
	RFC5	0.029	up	5.344	1.000	0.184	0.031	down	19.289	0.895	0.640