Table S1. List of genes differentially expressed genes in the IRX5:HCHL stems.
IRX5:HCHL(2) stem samples were analyzed using wild-type (WT) sample grown in the same conditions as a reference. Negative and
positive ratios indicate that the gene is down-regulated and up-regulated in transgenics, respectively (P < 0.05).
AGI Gene ID
Annotated Function
log2 ratio
IRX5:HCHL
/ WT
P value*
0.00E+0
MONOOXYGENASES
AT1G62570
flavin-containing monooxygenase family protein
1.13
AT3G28740
cytochrome P450 family protein
1.10
0.00E+0
AT4G15760
monooxygenase, putative (MO1)
0.86
7.69E-12
AT4G37370
CYP81D8
0.72
1.20E-7
AT3G28740
cytochrome P450 family protein
0.70
5.58E-7
AT2G12190
cytochrome P450, putative
0.65
8.60E-6
AT1G69500
CYP704B1
0.58
7.38E-4
AT3G14610
CYP72A7
0.51
2.96E-2
DEHYDROGENASES / REDUCTASES
AT4G13180
short-chain dehydrogenase/reductase (SDR) family protein
1.67
0.00E+0
AT2G37770
aldo/keto reductase family protein, Transcript variant 1
1.04
0.00E+0
AT2G37770
aldo/keto reductase family protein, Transcript variant 2
0.96
0.00E+0
AT2G29350
SAG13 (Senescence-associated gene 13); short-chain dehydrogenase/reductase (SDR) family protein
0.83
4.62E-11
AT1G14130
2-oxoglutarate and Fe(II)-dependent oxygenase superfamily protein
0.72
9.59E-8
AT1G72680
cinnamyl-alcohol dehydrogenase, putative
0.90
0.00E+0
AT1G60730
aldo/keto reductase family protein
0.65
8.30E-6
AT1G18020
FMN-linked oxidoreductases superfamily protein, Transcript variant 1
0.62
7.14E-5
AT1G18020
FMN-linked oxidoreductases superfamily protein, Transcript variant 2
0.59
4.38E-4
AT2G47130
short-chain dehydrogenase/reductase (SDR) family protein, Transcript variant 1
0.58
7.60E-4
AT2G47130
short-chain dehydrogenase/reductase (SDR) family protein, Transcript variant 2
0.58
8.36E-4
AT1G18020
FMN-linked oxidoreductases superfamily protein, Transcript variant 3
0.54
6.80E-3
AT5G14780
FDH (FORMATE DEHYDROGENASE); NAD binding / oxidoreductase, acting on the CH-OH group of donors
0.53
1.24E-2
AT1G54100
ALDH7B4 (ALDEHYDE DEHYDROGENASE 7B4); 3-chloroallyl aldehyde dehydrogenase
0.51
3.00E-2
UDP-GLUCOSYLTRANSFERASES
AT1G05560
UGT75B1
1.67
0.00E+0
AT2G15490
UGT73B4
1.26
0.00E+0
AT4G34138
UGT73B1
1.25
0.00E+0
AT2G30140
UGT87A2
0.79
5.31E-10
AT4G34131
UGT73B3
0.58
8.09E-4
AT3G11340
UGT76B1
0.58
8.97E-4
AT4G01070
UGT72B1
0.52
2.00E-2
TRANSPORTERS
AT3G23560
ALF5 (ABERRANT LATERAL ROOT FORMATION 5); antiporter/ transporter
1.18
0.00E+0
AT2G36380
PDR6 (PLEIOTROPIC DRUG RESISTANCE 6); ATPase, coupled to transmembrane movement of substances
1.13
0.00E+0
AT3G51860
CAX3 (cation exchanger 3); cation:cation antiporter
1.07
0.00E+0
AT5G65380
Multidrug and toxic compound extrusion (MATE) efflux family protein
0.92
0.00E+0
AT1G79410
ATOCT5 (organic cation/carnitine transporter 5)
0.89
0.00E+0
AT5G13750
ZIFL1 (ZINC INDUCED FACILITATOR-LIKE 1); tetracycline:hydrogen antiporter/ transporter
0.78
1.18E-9
AT1G76520
auxin efflux carrier family protein
0.70
4.27E-7
AT1G76530
auxin efflux carrier family protein
0.69
8.91E-7
AT4G18197
AT4G18200/PUP7 (purine permease 7); purine transporter
0.64
1.62E-5
AT4G28390
AAC3 (ADP/ATP CARRIER 3); ATP:ADP antiporter/ binding
0.62
6.57E-5
AT5G45380
DUR3 (DEGRADATION OF UREA 3); sodium:solute symporter family protein
0.61
1.05E-4
AT3G18830
PLT5 (POLYOL TRANSPORTER 5)
0.57
1.56E-3
AT2G17500
auxin efflux carrier family protein
0.55
3.26E-3
DETOXIFICATION
AT1G17170
ATGSTU24 (Glutathione S-transferase (class tau) 24)
1.32
0.00E+0
AT2G29420
ATGSTU7 (GLUTATHIONE S-TRANSFERASE 25)
1.22
0.00E+0
AT2G47730
ATGSTF8 (GLUTATHIONE S-TRANSFERASE 8)
1.16
0.00E+0
AT4G02520
ATGSTF2 (Glutathione S-transferase (class phi) 2)
0.78
2.04E-9
AT3G09270
ATGSTU8 (Glutathione S-transferase (class tau) 8)
0.65
1.43E-5
AT2G29490
ATGSTU1 (GLUTATHIONE S-TRANSFERASE 19)
0.54
7.21E-3
AT4G19880
unknown protein, Glutathione S-transferase family protein
0.76
6.73E-9
AT5G39050
ATPMaT1 (phenolic glucoside malonyltransferase 1); transferase family protein
0.77
3.95E-9
AT5G39090
ATPMaT1-like; transferase family protein
0.52
2.13E-2
JASMONIC ACID METABOLISM
AT1G76680
OPR1 (12-oxophytodienoate reductase 1)
1.27
0.00E+0
AT5G54206
12-oxophytodienoate reductase-related
0.99
0.00E+0
STRESS INDUCIBLE / DEFENSE / SENESCENCE
AT5G49480
ATCP1 (CA2+-BINDING PROTEIN 1); calcium ion binding, NaCl stress inducible
1.24
0.00E+0
AT1G35260
Bet v I allergen family protein, defense response
0.88
0.00E+0
AT3G62550
universal stress protein (USP) family protein, Adenine nucleotide alpha-like protein
0.87
0.00E+0
AT1G73500
ATMKK9 (Arabidopsis thaliana MAP kinase kinase 9)
0.80
3.62E-10
AT4G02380
SAG21 (SENESCENCE-ASSOCIATED GENE 21)
0.77
3.99E-9
AT3G04720
PR4 (PATHOGENESIS-RELATED 4), similar to the antifungal chitin-binding protein hevein
0.64
2.04E-5
AT1G75270
DHAR2; glutathione dehydrogenase (ascorbate)
0.61
1.17E-4
AT1G70530
CRK3 (CYSTEINE-RICH RLK (RECEPTOR-LIKE PROTEIN KINASE) 3), protein kinase family protein
0.60
2.36E-4
AT3G50970
LTI30/XERO2 (LOW TEMPERATURE-INDUCED 30); dehydrin stress-related
0.58
8.28E-4
AT5G27760
hypoxia-responsive family protein
0.54
6.87E-3
AT3G56710
SIB1 (SIGMA FACTOR BINDING PROTEIN 1); binding
0.51
2.30E-2
MISCELLANEOUS
Transcription factor
AT5G63790
ANAC102 (Arabidopsis NAC domain containing protein 102); transcription factor. Transcript variant 1
1.87
0.00E+0
AT1G77450
ANAC032 (Arabidopsis NAC domain containing protein 32); transcription factor
1.14
0.00E+0
AT5G63790
ANAC102 (Arabidopsis NAC domain containing protein 102); transcription factor. Transcript variant 2
0.65
1.26E-5
AT1G01720
ATAF1 (Arabidopsis NAC domain containing protein 2); transcription factor
0.54
7.23E-3
Glycine-rich protein
AT2G05380
GRP3S (GLYCINE-RICH PROTEIN 3 SHORT ISOFORM) Transcript variant 1
2.03
0.00E+0
AT2G05380
GRP3S (GLYCINE-RICH PROTEIN 3 SHORT ISOFORM) Transcript variant 2
1.03
0.00E+0
AT2G05530
glycine-rich protein
0.96
0.00E+0
AT2G05540
glycine-rich protein
0.90
0.00E+0
Auxin metabolism
AT3G44300
NIT2 (NITRILASE 2)
1.22
0.00E+0
AT3G44310
NIT1 (NITRILASE 1)
0.51
3.32E-2
Other
AT5G30870
transposable element gene; pseudogene, hypothetical protein
1.24
0.00E+0
AT3G14990
4-methyl-5(b-hydroxyethyl)-thiazole monophosphate biosynthesis protein, putative
1.20
0.00E+0
AT1G65280
heat shock protein binding / unfolded protein binding
1.07
0.00E+0
AT4G16190
cysteine proteinase, putative
0.89
0.00E+0
AT1G02850
glycosyl hydrolase family 1 protein BGLU11
0.86
7.69E-12
AT1G17860
trypsin and protease inhibitor family protein / Kunitz family protein
0.86
7.69E-12
AT3G49780
ATPSK4 (PHYTOSULFOKINE 4 PRECURSOR); growth factor
0.82
5.38E-11
AT2G41380
embryo-abundant protein-related, methyltransferase activity
0.82
6.15E-11
AT3G24420
hydrolase, alpha/beta fold family protein
0.79
1.07E-9
AT5G52810
ornithine cyclodeaminase/mu-crystallin family protein
0.67
2.65E-6
AT5G17380
pyruvate decarboxylase family protein
0.64
1.84E-5
AT1G23890
NHL repeat-containing protein
0.59
3.35E-4
AT4G28380
leucine-rich repeat family protein, zinc ion binding
0.59
3.52E-4
AT4G01870
tolB protein-related
0.59
4.41E-4
AT1G37130
NIA2 (NITRATE REDUCTASE 2)
0.62
6.75E-5
AT1G24610
SET domain-containing protein, unknown protein
0.58
9.14E-4
AT4G11600
ATGPX6 (GLUTATHIONE PEROXIDASE 6); glutathione peroxidase
0.52
1.83E-2
UNKNOWN
AT5G61820
unknown protein
1.68
0.00E+0
AT1G76600
unknown protein
1.18
0.00E+0
AT1G76960
unknown protein
0.71
2.01E-7
AT4G17840
unknown protein
0.67
2.77E-6
AT1G21680
unknown protein
0.61
1.38E-4
AT5G40960
unknown protein, DUF3339
0.59
5.08E-4
AT4G08555
unknown protein
0.58
8.16E-4
AT2G30690
unknown protein, DUF593
0.53
8.86E-3
AT5G66052
unknown protein
0.50
4.05E-2
AGI Gene ID
Annotated Function
log2 ratio
IRX5:HCHL
/ WT
P value*
CARBOHYDRATE METABOLISM
AT2G06850
EXGT-A1 (ENDO-XYLOGLUCAN TRANSFERASE); hydrolase, acting on glycosyl bonds
-0.51
2.51E-2
AT3G52840
BGAL2 (beta-galactosidase 2), Glycoside hydrolase family 35, putative lactase
-0.52
1.83E-2
AT3G01345
Glycoside hydrolase family 35, beta-galactosidase putative
-0.53
1.13E-2
AT3G53190
pectate lyase family protein
-0.56
1.69E-3
AT5G03350
legume lectin family protein, carbohydrate binding
-0.57
1.28E-3
AT1G26810
GALT1 (galactosyltransferase 1), Glycoside transferase family 31
-0.61
1.02E-4
AT1G19600
pfkB-type carbohydrate kinase family protein
-0.63
3.41E-5
AT4G28250
ATEXPB3 (ARABIDOPSIS THALIANA EXPANSIN B3)
-0.79
7.46E-10
AT3G30720
unknown protein, QUA-QUINE STARCH (QQS)
-1.08
0.00E+0
MISCELLANEOUS
AT4G27440
PORB (PROTOCHLOROPHYLLIDE OXIDOREDUCTASE B); protochlorophyllide reductase
-0.50
4.45E-2
AT5G02890
HXXXD-type acyl-transferase family protein
-0.50
3.86E-2
AT1G18950
aminoacyl-tRNA synthetase family
-0.51
3.29E-2
AT5G47330
palmitoyl protein thioesterase family protein
-0.53
1.07E-2
AT1G03870
FLA9 (FLA9)
-0.54
4.82E-3
AT1G20530
unknown protein, DUF630 and DUF632
-0.55
4.67E-3
ATCG00470
ATP SYNTHASE EPSILON CHAIN, rotational mechanism
-0.55
3.12E-3
AT5G51720
unknown protein, 2 iron, 2 sulfur cluster binding
-0.56
2.02E-3
ATCG00330
RPS14, CHLOROPLAST RIBOSOMAL PROTEIN S14
-0.58
8.70E-4
ATCG00340
D1 subunit of photosystem I and II reaction centers, Transcript variant 1
-0.62
5.42E-5
AT2G38870
serine-type endopeptidase inhibitor activity, pathogenesis-related peptide of the PR-6 proteinase inhibitor family
ATCG00340
D1 subunit of photosystem I and II reaction centers, Transcript variant 2
-0.64
-0.71
1.54E-5
2.75E-7
*To statistically analyze microarray data, the raw data comprised the logarithm of median feature pixel
intensity at wavelengths 635 nm (red) and 532 nm (green) for each array, and no background was subtracted. An
array-by-array normalization was performed to remove systematic biases. First, spots considered badly formed
features were excluded. Then a global intensity-dependent normalization using the loess procedure (Yang et al.,
2002) was performed to correct the dye bias. Finally, for each block, the log-ratio median calculated over the values
for the entire block was subtracted from each individual log-ratio value to correct print tip effects. Differential
analysis was based on the log ratios averaged on the dye-swap: The technical replicates were averaged to get one
log-ratio per biological replicate and these values were used to perform a paired t-test. A trimmed variance is
calculated from spots which do not displaying extreme variance (see details in Gagnot et al., 2008). The raw Pvalues were adjusted by the Bonferroni method, which controls the Family Wise Error Rate in order to keep a strong
control of the false positives in a multiple-comparison context. We considered as being differentially expressed the
probes with a Bonferroni P < 0.05.