Table 1.

Gene sets identified by the conventional method (blue) and CDBGE selector (green), related to Figure 2.

Conventional method
IFN-γ_LPS_Markers
Time	6 h		24 h		48 h
Gene	Log2FC	FDR	Log2FC	FDR	Log2FC	FDR
ACOD1	15.57	1.43·10−20	14.70	3.37·10−81	13.07	4.02·10−93
IDO1	14.10	1.03·10−258	13.80	2.66·10−197	13.80	3.58·10−285
BCL2L14	14.10	6.13·10−09	12.81	1.29·10−22	13.56	5.69·10−28
CXCL11	17.25	4.39·10−21	12.29	2.55·10−68	9.77	1.25·10−10
IL12B	17.22	1.26·10−14	12.76	3.23·10−40	8.96	9.43·10−07
SERPINB7	11.71	3.76·10−02	12.81	1.84·10−22	14.07	3.13·10−12
CSF3	13.70	1.27·10−02	12.45	8.89·10−07	12.03	7.59·10−06
UBD	12.78	3.41·10−07	11.61	3.65·10−10	12.56	1.98·10−16
CCL19	14.06	4.30·10−39	12.25	1.50·10−61	10.48	9.76·10−107
IL10_Markers
Time	6 h		24 h		48 h
Gene	Log2FC	FDR	Log2FC	FDR	Log2FC	FDR
CEMIP	6.41	2.19·10−04	7.23	1.51·10−04	5.24	1.62·10−03
CASP5	5.90	1.34·10−13	5.94	1.09·10−10	6.09	6.01·10−14
TNIP3	6.80	3.31·10−56	6.60	1.04·10−04	3.65	3.20·10−04
ARNT2	5.24	3.38·10−18	5.86	2.32·10−18	4.54	2.42·10−11
ENPP2	4.64	1.47·10−57	4.46	1.71·10−20	6.29	2.94·10−150
VCAN	4.38	2.70·10−23	3.89	5.63·10−12	4.10	1.90·10−02
MARCO	3.30	3.13·10−02	3.75	1.68·10−03	5.13	4.83·10−96
CCL18	3.70	1.06·10−09	3.72	9.41·10−10	4.50	1.99·10−30
FPR1	4.09	6.28·10−36	3.44	6.08·10−40	4.16	1.15·10−42
HepG2_Markers
Time	6 h		24 h		48 h
Gene	Log2FC	FDR	Log2FC	FDR	Log2FC	FDR
IL6	9.34	1.03·10−09	7.32	4.60·10−11	5.02	3.87·10−09
ANKRD22	3.79	1.95·10−02	3.07	2.74·10−02	3.79	2.68·10−09
ADGRE1	2.45	2.01·10−02	2.54	7.65·10−06	3.28	8.83·10−16
SOCS3	3.32	5.56·10−03	2.55	8.60·10−06	2.31	1.44·10−03
MYO1G	2.61	1.05·10−02	2.06	4.14·10−02	1.64	4.77·10−03
PTGIR	2.34	2.53·10−02	2.15	2.31·10−03	1.78	4.29·10−03
FCGR2A	1.96	7.40·10−03	1.88	9.71·10−03	2.28	4.49·10−06
ETS2	2.36	7.40·10−03	1.89	6.41·10−04	1.68	5.46·10−03
HSPA1A	1.78	1.67·10−02	1.39	2.74·10−02	1.06	3.21·10−03
CDBGE
IFN-γ_LPS_Markers
Time	6 h		24 h		48 h
Gene	Log2FC	FDR	Log2FC	FDR	Log2FC	FDR
CSAG3	7.24	6.44·10−03	7.27	1.68·10−04	7.82	8.23·10−07
CSF3	13.70	1.27·10−02	12.45	8.89·10−07	12.03	7.59·10−06
LINC01539	7.12	7.86·10−03	7.48	9.67·10−05	10.10	2.64·10−14
SERPINB7	11.71	3.76·10−02	12.81	1.84·10−22	14.07	3.13·10−12
BCL2L14	14.10	6.13·10−09	12.81	1.29·10−22	13.56	5.69·10−28
IDO1	14.10	1.03·10−258	13.80	2.66·10−197	13.80	3.58·10−285
AMOTL2	12.80	2.13·10−02	10.40	5.43·10−14	8.84	4.85·10−10
ACOD1	15.57	1.43·10−20	14.70	3.37·10−81	13.07	4.02·10−93
IDO2	1.65	2.24·10−06	10.29	2.01·10−14	11.24	7.89·10−19
IL10_Markers
Time	6 h		24 h		48 h
Gene	Log2FC	FDR	Log2FC	FDR	Log2FC	FDR
TUBB3	3.28	1.12·10−14	3.46	1.47·10−36	2.68	1.15·10−10
TDO2	3.70	2.60·10−06	4.23	1.16·10−08	2.80	2.38·10−05
CD163	2.09	5.00·10−10	2.48	1.22·10−10	2.92	6.17·10−29
VWA1	3.23	1.88·10−08	2.58	3.55·10−04	2.41	2.59·10−04
GPR85	3.66	2.24·10−04	3.24	7.13·10−04	2.81	1.28·10−2
FPR1	4.09	6.28·10−36	3.44	6.08·10−40	4.16	1.15·10−42
MARCO	3.30	3.13·10−02	3.75	1.68·10−03	5.13	4.83·10−96
PKIB	2.21	6.25·10−04	2.43	2.79·10−06	2.52	8.18·10−09
FCGR3B	1.88	2.68·10−06	2.32	1.06·10−07	2.58	1.87·10−18
HepG2_Markers
Time	6 h		24 h		48 h
Gene	Log2FC	FDR	Log2FC	FDR	Log2FC	FDR
IL6	9.34	1.03·10−09	7.32	4.60·10−11	5.02	3.87·10−09
ANKRD22	3.79	1.95·10−02	3.07	2.74·10−02	3.79	2.68·10−09
ADGRE1	2.45	2.01·10−02	2.54	7.65·10−06	3.28	8.83·10−16
SOCS3	3.32	5.56·10−03	2.55	8.60·10−03	2.31	1.44·10−03
MYO1G	2.61	1.05·10−02	2.06	4.14·10−02	1.64	4.77·10−03
PTGIR	2.34	2.53·10−02	2.15	2.21·10−03	1.78	4.29·10−03
FCGR2A	1.96	7.40·10−03	1.88	9.71·10−03	2.28	4.49·10−06
ETS2	2.36	7.40·10−03	1.89	6.41·10−04	1.68	5.46·10−03
HSPA1A	1.78	1.67·10−02	1.39	2.74·10−02	1.06	3.21·10−03

Log₂FC and FDR values are shown for different cell types at various time points.