Improved biomarker discovery through a plot twist in transcriptomic data analysis

Table 2 Comparison of model fit parameters under different soft thresholds using methods #3 (DEGs + WGCNA) and #4 (WGCNA + DEGs) on the gonadal transcriptome during early sex differentiation in three different species: sea bass, mouse, and human. The selected threshold and results obtained with the selected threshold are shown in bold

	Method	Threshold	Signed R² (model fit)	Mean connectivity	Slope	R²
	Method	Threshold	Signed R² (model fit)	Mean connectivity	(scale-free topology)
Dicentrarchus labrax	#3 DEGs + WGCNA	5	0.19	1580	− 0.12	0.08
		7	0.63	1100	− 0.33	0.59
		9	0.7	800	− 0.47	0.73
		11	0.8	650	− 0.56	0.79
		13	0.8	450	− 0.64	0.81
	#4 WGCNA + DEGs	5	0.89	2050	− 0.51	0.82
		7	0.9	1400	− 0.63	0.87
		9	0.91	900	− 0.71	0.88
		11	0.9	700	− 0.78	0.87
		13	0.9	500	− 0.83	0.86
Mus musculus	#3 DEGs + WGCNA	8	0.13	540	0.02	− 0.3
		10	0.33	375	− 0.5	0.24
		12	0.47	300	− 0.65	0.4
		14	0.55	230	− 0.79	0.51
		16	0.62	180	− 0.89	0.57
	#4 WGCNA + DEGs	8	0.62	495	− 0.62	0.4
		10	0.67	325	− 0.77	0.49
		12	0.7	220	− 0.88	0.55
		14	0.7	200	− 0.96	0.59
		16	0.73	160	− 1.02	0.62
Homo sapiens	#3 DEGs + WGCNA	4	0.45	105	− 0.74	0.38
		6	0.61	50	− 0.93	0.56
		8	0.67	25	− 1.02	0.63
		10	0.68	19	− 1.1	0.64
		12	0.69	15	− 1.17	0.65
	#4 WGCNA + DEGs	4	0.7	950	− 1.3	0.66
		6	0.79	410	− 1.36	0.77
		8	0.89	210	− 1.38	0.87
		10	0.93	100	− 1.42	0.92
		12	0.95	85	− 1.45	0.95

ISSN: 1741-7007