Table 2.

List of genes downregulated 2 h after treatment with IAA

Category	At no.	Probe ID	Gene title	IAA		IAA + Dex		Impaired in arf mutantse	AuxRE
				FCa	P-valueb	FCc	P-valued		Af	Bg
Auxin-regulated	At4g31320	253515_at	Small auxin up RNA (SAUR_C)	0.28	0.034	1.18	0.012	√	1	0
	At4g17280	245412_at	Auxin-responsive protein	0.45	0.013	0.73	0.036		0	1
Boitic and abiotic	At5g45210	248990_at	Disease resistance protein	0.28	5.46E-04	0.52	0.157		0	1
	At4g39030	252921_at	Salicylic acid induction deficient 1 (SID1)	0.49	0.007	0.78	0.070		1	1
	At1g73620	260077_at	Pathogenesis-related protein	0.49	0.039	0.56	0.637		0	0
Development	At2g20750	265443_at	β-expansin (EXPB1)	0.27	0.024	0.73	0.066		3	0
	At4g36380	246216_at	Rotundifolia3 (ROT3)(CYP90C1)	0.35	0.002	0.68	0.002	√	1	2
Metabolism	At1g05660	263229_s_at	Polygalacturonase	0.03	0.022	1.13	0.014		3	0
	At1g64590	261956_at	Short-chain dehydrogenase (SDR)	0.22	0.006	0.97	0.008	√	1	1
	At1g67110	264470_at	Cytochrome P450 protein (CYP735A2)	0.27	1.80E-04	0.62	0.068		1	0
	At4g13310	254767_s_at	Cytochrome P450 protein (CYP71A19)	0.27	0.038	0.54	0.118		0	1
	At5g47990	248727_at	Cytochrome P450 protein (CYP705A5)	0.29	0.040	0.76	0.101		3	0
	At2g43880	267222_at	Polygalacturonase	0.34	0.010	0.82	0.038		0	3
	At4g21840	254385_s_at	Methionine sulfoxide reductase	0.35	0.019	0.67	0.061		0	2
	At1g78090	260059_at	Trehalose-6-phosphate phosphatase	0.39	0.017	0.85	0.029		2	1
	At5g42590	249203_at	Cytochrome P450 protein (CYP71A16)	0.39	0.050	1.35	0.060		2	2
	At4g39950	252827_at	Cytochrome P450 protein (CYP79B2)	0.41	0.003	0.62	0.041	√	0	2
	At4g11290	254914_at	Peroxidase	0.45	0.040	0.72	0.178		3	0
	At5g58784	247781_at	Dehydrodolichyl diphosphate synthase	0.48	0.047	0.55	0.359		1	0
	At2g23560	267123_at	Hydrolase	0.49	0.004	0.94	0.077		0	0
Protein metabolism	At3g20015	256626_at	Aspartyl protease	0.43	0.028	0.84	0.060		0	0
Signal transduction	At5g62920	247406_at	ARR6	0.22	0.017	0.71	0.038		1	0
	At3g48100	252374_at	ARR5	0.24	0.039	0.57	0.080		1	3
	At5g24100	249768_at	LRR protein kinase	0.25	0.017	0.56	0.092		3	1
	At1g19050	259466_at	ARR7	0.43	0.038	0.47	0.689		3	1
	At1g10470	263236_at	ARR4	0.49	0.011	0.74	0.038		0	2
Transcription factor	At1g10480	263208_at	ZFP5	0.21	0.007	0.96	0.005		1	1
	At3g46130	252534_at	MYB111	0.31	0.042	1.09	0.080		0	4
	At5g25160	246933_at	ZFP3	0.34	0.003	0.83	7.52E-04		1	3
	At1g72200	259854_at	Zinc finger (C3HC4-type) protein	0.50	0.013	0.95	0.020	√	2	0
Transferase	At2g18800	266066_at	Xyloglucan:xyloglucosyl transferase	0.08	0.020	0.56	0.035		1	0
	At4g12510	254820_s_at	Lipid transfer protein (LTP)	0.15	0.008	0.54	0.010	√	0	0
	At5g47980	248725_at	Transferase	0.17	0.004	0.65	0.010		1	2
	At1g77530	259758_s_at	O-methyltransferase 2	0.21	0.008	0.69	0.021		0	1
	At5g47950	248723_at	Transferase	0.34	1.48E-04	0.82	0.038		0	2
	At1g80050	262039_at	Adenine phosphoribosyltransferase 2 (APT2)	0.39	0.004	0.66	0.016	√	1	0
	At1g53680	259964_at	Glutathione S-transferase (AtGSTU28)	0.39	0.023	0.74	0.026	√	0	0
	At3g45070	252605_s_at	Sulphotransferase	0.40	0.021	1.06	0.066		1	0
	At3g29680	257281_s_at	Transferase	0.40	0.007	0.75	0.076		2	0
	At3g08860	258983_at	Alanine-glyoxylate aminotransferase	0.44	0.045	1.02	0.060		0	0
	At2g23410	267137_at	cis-Prenytransferase	0.46	0.016	0.26	0.213		3	1
Transporter	At5g47450	248790_at	Major intrinsic protein (TIP2;3)	0.27	0.020	0.84	0.032	√	1	2
	At5g60660	247586_at	PIP2:4	0.28	0.007	0.73	0.025	√	0	0
	At3g45680	252594_at	Oligopeptide transporter	0.31	9.04E-04	0.70	0.017		0	2
	At1g31770	246580_at	ABC transporter	0.35	0.007	0.76	0.002		2	1
	At3g23430	258293_at	Phosphate transporter (PHO1)	0.42	0.005	0.89	6.51E-04		0	0
Unknown	At4g26320	253957_at	Arabinogalactan-protein (AGP13)	0.16	0.007	0.46	0.071	√	1	1
	At5g60520	247634_at	Late embryogenesis abundant protein	0.19	0.027	0.55	0.133	√	0	0
	At5g53250	248252_at	Arabinogalactan-protein (AGP22)	0.29	0.018	0.53	0.116	√	2	2
	At4g02850	255450_at	PhzC/PhzF family protein	0.33	0.019	0.61	0.065		0	0
	At3g21680	258178_at	Expressed protein	0.34	0.038	1.12	0.016		1	2
	At4g30460	253619_at	Glycine-rich protein	0.37	0.031	0.84	0.003		0	1
	At2g21560	263545_at	Expressed protein	0.37	0.019	0.88	0.029		0	2
	At5g28610	255945_at	Expressed protein	0.38	0.031	0.56	0.457		1	2
	At3g46880	252501_at	Expressed protein	0.39	0.004	0.65	0.036		0	2
	At5g03960	250872_at	Calmodulin-binding protein	0.42	0.015	1.01	0.015		1	2
	At5g19970	246142_at	Expressed protein	0.42	0.003	0.86	0.005		1	0
	At1g31050	265160_at	Expressed protein	0.44	0.035	0.89	0.055		2	2
	At2g09970	260453_s_at	Expressed protein	0.47	0.007	0.93	0.023		0	1

^aFold change of gene expresion in auxin-treated 7-d-old iaa1:GR transgenic plants compared to that of mock-treated plants.

^bP-value calculated from auxin-down-regulated gene expression and mock expression using Welch's t-test.

^cFold change of gene expresion in auxin and DEX-treated 7-d-old iaa1:GR transgenic plants compared to that of mock-treated plants.

^dP-value calculated from auxin-down-regulated gene expression in the presence of DEX and auxin-down-regulated gene expression using Welch's t-test.

^eGenes showing auxin-induced expression impaired in nph4-1 and/or arf19-1 and/or nph4-1 arf19-1 mutants by microarray analysis (Okushima et al., 2005).

^fNumber of AuxRE, TGTCnC sequences in the 2 kb fragments upstream of the start codon.

^gNumber of AuxRE, GnGACA sequences in the 2 kb fragments upstream of the start codon.