Prediction of genomic biomarkers for endometriosis using the transcriptomic dataset

Table 1 The results of the bioinformatics analysis

ID	Gene symbol	Adjust P value	P value	t	Log2FC	Diff. expressed
ENSG00000226925	IL1R1-AS1	0.08254818	0.0000092762	5.1238	1.5643	Up
ENSG00000149201	CCDC81	0.08254818	0.0000105433	5.2962	1.2448	Up
ENSG00000091972	CD200	0.08254818	0.0000300938	4.7445	1.4053	Up
ENSG00000143320	CRABP2	0.08254818	0.0000141606	-5.8310	-1.3148	Down
ENSG00000011243	AKAP8 L	0.08254818	0.0000572588	-4.5349	-1.1421	Down
ENSG00000138075	ABCG5	0.08254818	0.0000608491	4.5150	0.9750	No
ENSG00000226807	MROH5	0.08254818	0.0000663279	-4.5179	-1.7847	Down
ENSG00000158220	ESYT3	0.08254818	0.0000758312	4.4428	1.4350	Up
ENSG00000170852	KBTBD2	0.08254818	0.0000796663	4.4265	0.8138	No
ENSG00000164190	NIPBL	0.08254818	0.0000805697	4.4228	0.7743	No

FC: Fold change.

Table 2 Descriptive statistics for input variables¹

Gene ID	Gene symbol	Median		OR	P
		Normal (n = 22)	Endometriosis (n = 16)
ENSG00000085741	WNT11	1 (0-6)	0 (0-2)	-	0.093
ENSG00000103966	EHD4	10 (2-39)	4.5 (0-28)	0.828	< 0.0001
ENSG00000105374	NKG7	4 (0-15)	1 (0-7)	0.619	0.003
ENSG00000111249	CUX2	2 (0-6)	0 (0-1)	0.151	< 0.0001
ENSG00000139880	CDH24	1 (0-5)	0 (0-2)	0.145	< 0.0001
ENSG00000141577	CEP131	5 (1-14)	2 (0-9)	0.545	< 0.0001
ENSG00000158014	SLC30A2	1 (0-60)	1 (0-8)	-	0.637
ENSG00000166250	CLMP	7 (1-11)	12 (8-38)	2.617	< 0.0001
ENSG00000180385	EMC3-AS1	20 (10-40)	14 (2-20)	0.751	< 0.0001
ENSG00000183729	No found	1 (0-39)	0 (0-39)	-	0.166
ENSG00000196821	ILRUN	4 (1-8)	2 (0-7)	0.682	0.021
ENSG00000201207	Y_RNA	11.5 (3-25)	6 (1-12)	0.802	0.012
ENSG00000211935	IGHV1-3	1 (0-12)	0 (0-3)	-	0.022
ENSG00000226715	LINC01709	19 (0-53)	36 (3-84)	1.050	0.014
ENSG00000228630	HOTAIR	3 (0-12)	1 (0-5)	0.603	0.009
ENSG00000229245	No found	1 (0-35)	23.5 (0-59)	1.100	< 0.0001
ENSG00000232153	Novel transcript	31 (2-631)	323 (36-926)	1.007	0.000
ENSG00000256249	Novel transcript	8.5 (1-1653)	3 (0-22)	-	0.011
ENSG00000264630	PRKCA-AS1	0 (0-2)	1.5 (0-19)	2.812	0.003
ENSG00000270591	PPP2R5C	1 (0-3)	3 (0-8)	2.736	< 0.0001
ENSG00000279271	TEC	1 (0-9)	10 (0-45)	1.486	< 0.0001

¹Continuous variables are given as median (min-max).

Table 3 The results of performance metrics for the model

	AdaBoost	XGBoost	Stochasting Gradient Boosting	Bagged CART
Accuracy	71.4	85.7	71.4	85.7
Balanced accuracy	70.8	83.3	66.7	85.7
Sensitivity	66.7	66.7	33.3	100
Specificity	75.0	100	100	75
PPV	66.7	100	100	75
NPV	75.0	80.0	66.7	100
F1 score	66.7	80.0	50.0	85.7

CART: Classification and regression trees; PPV: Positive predictive value; NPV: Negative predictive value.