Table 3.

Top ranking features from the RF model trained on the genes-only dataset (Left). Top ranking features with p-values less than 0.05 and their importance scores discovered by our genes model (Left). Side-paired differential expression (fold change) analysis results of TPM values for the same features (Right) Wilcoxon-rank sum test was used to calculate p-values and FDR (Benjamini & Hochberg)

Model Feature Importance Metrics					Differential Expression
Rank	Ensemble ID_Gene ID	Importance Score	Log Importance Score	p-value	Log2 FC	p-value	FDR	Greater Expr. Side
1	ENSG00000159182_PRAC1	0.12	-2.16	0	-2.86	5.08E-21	3.10E-19	Left
2	ENSG00000159184_HOXB13	0.07	-2.7	0	-1.78	1.78E-11	2.18E-10	Left
3	ENSG00000144451_SPAG16	0.05	-3.04	0	-0.64	9.00E-09	4.99E-08	Left
4	ENSG00000198353_HOXC4	0.05	-3.08	0	1.88	2.11E-15	6.43E-14	Right
5	ENSG00000184719_RNLS	0.03	-3.36	0	-0.89	2.85E-10	2.48E-09	Left
6	ENSG00000145649_GZMA	0.03	-3.42	0	1.54	4.75E-07	1.93E-06	Right
7	ENSG00000197757_HOXC6	0.02	-3.84	0	1.28	5.02E-12	1.02E-10	Right
8	ENSG00000162409_PRKAA2	0.02	-3.87	0	-1.2	3.90E-10	2.97E-09	Left
9	ENSG00000037965_HOXC8	0.02	-3.87	0	1.32	7.90E-12	1.20E-10	Right
10	ENSG00000147457_CHMP7	0.02	-3.92	0	0.35	8.44E-06	2.71E-05	Right
11	ENSG00000165548_TMEM63C	0.02	-3.99	0	-0.83	5.31E-05	0.000147	Left
12	ENSG00000203880_PCMTD2	0.02	-4.01	0	-0.43	5.16E-08	2.62E-07	Left
13	ENSG00000119397_CNTRL	0.02	-4.08	0.01	0.27	1.84E-06	7.00E-06	Right
14	ENSG00000103485_QPRT	0.02	-4.09	0.01	-1.01	2.20E-10	2.24E-09	Left
15	ENSG00000170677_SOCS6	0.02	-4.13	0.03	0.39	4.14E-06	1.40E-05	Right