Table 4. Expression changes in auxin-pathway genes significantly upregulated or downregulated by WOX1 (FDR <0.05).

Description	Gene name	AGI code	Fold change (D/M)*1		p-value*2	q-value*3	Fold change (D/M+C)*1		ProbeName
			Mean	SE			Mean	SE
Biosynthesis	TAA1	AT1G70560	1.03	0.06	0.001	0.024	0.10	0.05	A_84_P19052
	TAR2	AT4G24670	−1.41	0.11	0.001	0.027	−0.70	0.12	A_84_P10057
	YUC1	AT4G32540	0.50	0.02	0.000	0.020	0.02	0.08	A_84_P22386
	YUC2	AT4G13260	−2.01	0.17	0.002	0.030	−0.91	0.37	A_84_P16644
	YUC4	AT5G11320	0.77	0.08	0.004	0.038	−0.10	0.47	A_84_P767924
			0.76	0.05	0.001	0.025	−0.59	0.07	A_84_P18684
	YUC5	AT5G43890	−3.74	0.15	0.000	0.019	−3.03	0.23	A_84_P23485
	NIT1	AT3G44310	0.71	0.05	0.001	0.025	0.22	0.13	A_84_P808866
			0.64	0.07	0.004	0.037	0.15	0.09	A_84_P21247
	NIT3	AT3G44320	1.74	0.11	0.001	0.025	1.23	0.06	A_84_P22193
	NIT4	AT5G22300	−1.42	0.09	0.001	0.024	−1.21	0.16	A_84_P10196
	CYP83B1	AT4G31500	−0.45	0.04	0.002	0.028	−0.13	0.06	A_84_P16706
Transport	AUX1	AT2G38120	0.74	0.09	0.005	0.041	0.12	0.05	A_84_P107652
	LAX1	AT5G01240	0.75	0.03	0.000	0.019	0.28	0.10	A_84_P859674
			0.94	0.10	0.003	0.036	0.45	0.05	A_84_P20541
	PIN1	AT1G73590	1.03	0.08	0.001	0.027	0.10	0.05	A_84_P11175
	PIN3	AT1G70940	−0.50	0.06	0.005	0.041	−0.19	0.06	A_84_P13326
	PIN7	AT1G23080	−1.08	0.08	0.001	0.027	−0.69	0.25	A_84_P67534
Activator ARF	MP	AT1G19850	1.42	0.04	0.000	0.017	0.23	0.06	A_84_P21913
Repressor ARF	ARF1	AT1G59750	0.16	0.00	0.000	0.017	0.01	0.01	A_84_P18037
	ARF6	AT1G30330	−0.29	0.03	0.005	0.041	−0.37	0.06	A_84_P21873
	ARF16	AT4G30080	0.36	0.01	0.000	0.017	0.29	0.06	A_84_P101526

*¹ Means of log₂ fold changes for four experiments; D/M indicates DEX/Mock; +C indicates “with CHX”. *² p-values as assessed by a two-sided t-test. *³ False discovery rate as assessed by the Benjamini–Hochberg method.