Table 4.

Gene sets enriched in phenotype.

Gene set name	Set size	Enrichment score	NES	NOM P	p-Adjust	FDR q
High expression
REACTOME_PD_1_SIGNALING	23	<0.001	<0.001	<.001	0.008	0.006
BIOCARTA_CTLA4_PATHWAY	20	<0.001	<0.001	<.001	0.008	0.006
KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY	75	<0.001	<0.001	<.001	0.008	0.006
KEGG_APOPTOSIS	87	<0.001	<0.001	<.001	0.008	0.006
REACTOME_SIGNALING_BY_FGFR	86	0.522	1.728	<.001	0.008	0.006
KEGG_JAK_STAT_SIGNALING_PATHWAY	154	<0.001	<0.001	.001	0.008	0.006
Low expression
REACTOME_INTERLEUKIN_21_SIGNALING	10	−0.852	−1.99	<.001	0.039	0.031
BIOCARTA_IL5_PATHWAY	11	−0.8254	−2.015	<.001	0.039	0.031
REACTOME_INTERLEUKIN_2_SIGNALING	12	−0.76774	−1.90938	<.001	0.039	0.031
BIOCARTA_MTA3_PATHWAY	18	−0.67389	−1.85959	<.001	0.039	0.031
BIOCARTA_CD40_PATHWAY	15	−0.71742	−1.86772	<.001	0.039	0.031
BIOCARTA_IL17_PATHWAY	15	−0.7526	−1.95831	<.001	0.039	0.031

FDR q-values, which is the probability estimate of possible false positive results for NES; Differences in gene sets with NOM P-value <.05 and FDR q-values <0.05 were considered statistically significant.

FDR = false discovery rate, NES = normalized enrichment score, NOM = nominal.