Acquired mutations and transcriptional remodeling in long-term estrogen-deprived locoregional breast cancer recurrences

Table 2 Differentially expressed genes in ESR1-depleted recurrences

Gene	Log2FC	*voom* average expression	Nominal p value	FDR-adjusted p value
*PAPPA*	1.395	6.416	0.001	0.293
*KLK7*	5.422	1.158	0.001	0.293
*PROM1*	3.931	5.005	0.002	0.588
*RASGRF1*	2.307	4.106	0.002	0.588
*DKK1*	2.732	0.473	0.004	0.614
*EPHB6*	1.641	3.819	0.005	0.614
*ABCC3*	1.637	8.010	0.006	0.614
*FGFR4*	1.515	5.267	0.010	0.695
*FBN2*	1.010	5.326	0.010	0.695
*TENM1*	1.326	4.709	0.012	0.705
*COL9A3*	2.034	2.249	0.014	0.705
*NDRG1*	1.218	8.945	0.014	0.705
*TP63*	2.135	4.441	0.018	0.768
*SCN8A*	1.290	5.881	0.019	0.768
*KIT*	1.289	6.020	0.020	0.768
*TCL6*	2.228	−0.254	0.022	0.790
*WNT11*	1.585	1.256	0.024	0.823
*SOCS1*	1.534	0.387	0.033	0.911
*HOXD11*	2.755	−1.369	0.034	0.911
*PLAG1*	1.275	4.576	0.036	0.911
*DTX4*	1.185	5.711	0.036	0.911
*FLNC*	1.588	6.787	0.037	0.911
*ALDOC*	1.494	5.224	0.039	0.911
*ACSBG1*	1.843	0.601	0.042	0.915
*SYP*	1.348	0.862	0.045	0.915
*ESR1*	− 3.952	9.492	0.000	0.146
*ATP8A2*	− 2.599	4.510	0.003	0.588
*ELOVL2*	− 2.090	2.413	0.006	0.614
*RABEP1*	− 1.009	10.352	0.012	0.705
*EYA1*	− 1.494	2.203	0.013	0.705
*IGF1R*	− 1.149	9.083	0.016	0.747
*CAMK2A*	− 1.391	2.742	0.016	0.747
*RERG*	− 1.413	6.562	0.018	0.768
*BCL2*	− 1.055	6.619	0.020	0.768
*FGF14*	− 1.393	2.430	0.023	0.790
*RASGRP1*	− 1.044	6.799	0.027	0.857
*BHLHE22*	− 1.822	0.822	0.035	0.911
*ZNF703*	− 1.811	4.865	0.038	0.911
*MYB*	− 1.179	8.857	0.045	0.915

ISSN: 1465-542X