TABLE 1

Geneset Enrichment Analysis for SARS-CoV-2 versus uninfected DE genes using Molecular Signatures Database (MSigDB) Hallmark gene sets

Geneset Name^#,¶	N Genes⁺	Direction^§	two-sided directional		non-directional
Geneset Name^#,¶	N Genes⁺	Direction^§	p-valueƒ	FDR^##	p-value^ƒ	FDR^##
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY	13	Up	6.92	2.74	2.61	6.92
HALLMARK_COMPLEMENT	76	Up	6.60	23.44	21.74	6.60
HALLMARK_KRAS_SIGNALING_DN	40	Down	6.60	11.03	10.67	6.60
HALLMARK_IL6_JAK_STAT3_SIGNALING	73	Up	6.46	19.71	18.62	6.46
HALLMARK_UNFOLDED_PROTEIN_RESPONSE	16	Up	6.37	2.47	2.35	6.37
HALLMARK_APOPTOSIS	79	Up	6.37	17.81	17.02	6.37
HALLMARK_OXIDATIVE_PHOSPHORYLATION	33	Up	5.25	5.28	5.05	5.25
HALLMARK_P53_PATHWAY	56	Up	4.98	16.44	15.69	4.98
HALLMARK_MTORC1_SIGNALING	47	Up	4.84	12.27	11.85	4.84
HALLMARK_INTERFERON_GAMMA_RESPONSE	110	Up	4.84	13.77	13.25	4.84
HALLMARK_PROTEIN_SECRETION	10	Up	4.78	1.14	1.11	4.78
HALLMARK_GLYCOLYSIS	48	Up	4.75	14.00	13.44	4.75
HALLMARK_PANCREAS_BETA_CELLS	5	Down	4.59	0.09	0.09	4.59
HALLMARK_HYPOXIA	60	Up	4.55	18.84	17.84	4.55
HALLMARK_MYC_TARGETS_V2	8	Up	4.49	0.25	0.24	4.49
HALLMARK_CHOLESTEROL_HOMEOSTASIS	15	Up	4.33	1.83	1.77	4.33
HALLMARK_INTERFERON_ALPHA_RESPONSE	52	Up	4.33	8.74	8.41	4.33
HALLMARK_SPERMATOGENESIS	19	Down	3.68	1.59	1.54	3.68
HALLMARK_MYC_TARGETS_V1	28	Up	3.60	4.40	4.22	3.60
HALLMARK_KRAS_SIGNALING_UP	77	Up	3.38	16.13	15.43	3.38
HALLMARK_ADIPOGENESIS	30	Up	3.30	4.88	4.67	3.30
HALLMARK_COAGULATION	56	Up	3.05	15.14	14.49	3.05
HALLMARK_XENOBIOTIC_METABOLISM	36	Up	2.98	11.63	11.25	2.98
HALLMARK_ANDROGEN_RESPONSE	16	Up	2.86	2.24	2.14	2.86
HALLMARK_FATTY_ACID_METABOLISM	20	Up	2.79	4.63	4.44	2.79
HALLMARK_APICAL_JUNCTION	61	Up	2.69	18.58	17.70	2.69
HALLMARK_UV_RESPONSE_UP	46	Up	2.68	12.07	11.67	2.68
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION	81	Up	2.64	14.94	14.32	2.64
HALLMARK_ESTROGEN_RESPONSE_EARLY	40	Up	2.60	8.46	8.16	2.60
HALLMARK_TGF_BETA_SIGNALING	20	Up	2.53	3.35	3.20	2.53
HALLMARK_ESTROGEN_RESPONSE_LATE	51	Up	2.51	12.47	12.01	2.51
HALLMARK_DNA_REPAIR	27	Up	1.99	5.96	5.71	1.99
HALLMARK_MITOTIC_SPINDLE	27	Up	1.94	3.12	2.98	1.94
HALLMARK_IL2_STAT5_SIGNALING	85	Up	1.81	14.68	14.10	1.81
HALLMARK_ANGIOGENESIS	19	Up	1.81	2.23	2.13	1.81
HALLMARK_UV_RESPONSE_DN	44	Up	1.78	8.73	8.41	1.78
HALLMARK_HEDGEHOG_SIGNALING	12	Up	1.75	0.98	0.96	1.75
HALLMARK_G2M_CHECKPOINT	67	Up	1.70	12.43	11.99	1.70
HALLMARK_APICAL_SURFACE	13	Up	1.68	1.32	1.28	1.68
HALLMARK_TNFA_SIGNALING_VIA_NFKB	107	Up	1.57	13.21	12.71	1.57
HALLMARK_INFLAMMATORY_RESPONSE	115	Up	1.49	20.51	19.29	1.49
HALLMARK_E2F_TARGETS	61	Up	1.46	8.04	7.76	1.46
HALLMARK_NOTCH_SIGNALING	21	Up	1.26	3.71	3.54	1.26
HALLMARK_MYOGENESIS	35	Up	1.11	7.37	7.11	1.11
HALLMARK_PI3K_AKT_MTOR_SIGNALING	56	Up	1.11	18.55	17.70	1.11
HALLMARK_PEROXISOME	17	Up	0.80	2.12	2.04	0.80
HALLMARK_ALLOGRAFT_REJECTION	141	Up	0.42	22.32	20.92	0.42
HALLMARK_WNT_BETA_CATENIN_SIGNALING	27	Up	0.38	5.58	5.34	0.38
HALLMARK_BILE_ACID_METABOLISM	14	Down	0.25	1.79	1.73	0.25
HALLMARK_HEME_METABOLISM	19	Up	0.04	2.19	2.10	0.04

All p-value and FDR reported as −log10 value.

^#Geneset signatures in green are enriched in SARS-CoV-2 compared to control (i.e. Direction is Up) while red is the opposite direction (i.e. Down);

^¶Genesets highlighted in yellow indicates biological processed upregulated in SARS-CoV-2 infected lungs. List ordered by descending FDR;

⁺N-Genes, number of genes in the geneset;

^§Direction, direction of change (i.e. up or down);

^ƒp-value, statistical significance of the difference;

^##FDR, false discovery rate.