Table 1. Top 10 transcription factor target gene sets from pathway analysis (GSEA) in each study population.

Transcription factor target gene sets	Number of genes	P-value	FDR
Discovery study population (2196 cases/4396 controls)
V$PAX8_B	92	0	0.21
GGARNTKYCCA_UNKNOWN	70	0	0.21
V$SOX5_01	241	0	0.31
RRAGTTGT_UNKNOWN	232	0	0.33
V$SRY_02	230	0	0.35
V$AP1_Q2	251	0	0.38
V$SRF_Q5_01	196	0	0.41
V$RSRFC4_Q2	199	0.001	0.39
AAANWWTGC_UNKNOWN	180	0.001	0.39
YAATNRNNNYNATT_UNKNOWN	100	0.002	0.22
Replication study population (7035 cases/21 693 controls)
CAGNYGKNAAA_UNKNOWN	68	0	0.15
V$MAF_Q6	231	0	0.37
V$E2F_01	60	0.001	0.16
V$YY1_01	218	0.002	0.42
V$CART1_01	202	0.003	0.38
V$PPARA_01	36	0.004	0.24
V$PAX8_B	91	0.004	0.37
TCCATTKW_UNKNOWN	210	0.004	0.43
V$IRF2_01	108	0.005	0.43
YKACATTT_UNKNOWN	258	0.005	0.52
Combined study population (9627 cases/30 845 controls)
V$PAX8_B	91	0	0.21
TTGCWCAAY_V$CEBPB_02	55	0	0.24
YAATNRNNNYNATT_UNKNOWN	98	0	0.27
YCATTAA_UNKNOWN	501	0	0.46
V$POU3F2_01	89	0.001	0.19
V$IRF2_01	108	0.001	0.28
V$CART1_01	202	0.001	0.43
V$OCT1_04	201	0.001	0.44
CAGNYGKNAAA_UNKNOWN	68	0.002	0.17
V$NKX25_01	112	0.002	0.28

Abbreviations: FDR=false discovery rate; GSEA=gene set enrichment analysis.