Table III. The most differentially expressed genes in roots

Of all the differentially expressed genes, only those with at least 2-fold changes, and maximal 15 genes for each different response pattern, are listed. Expression changes are given as log2. Expression changes in boldface correspond to genes differentially expressed at the significance threshold of Bonferroni P < 0.05. md, Missing data.

Arabidopsis Genome Initiative No.Gene DescriptionRootShoot
0 to 2 d2 to 10 d0 to 10 d0 to 2 d2 to 10 d0 to 10d
Transiently differentially expressed at day 2
 AT4G23700ATCHX17; monovalent cation:proton antiporter1.20−0.200.03−0.060.03−0.04
 AT2G36690Oxidoreductase−1.130.34−0.26−0.02−0.100.05
Rapidly changed and stayed high/low
 AT3G03910Oxidoreductase; Glu dehydrogenase, putative1.360.441.930.090.591.46
 AT1G70260Unknown protein; nodulin MtN21 family protein1.330.201.411.14−0.100.73
 AT1G77120ADH1 (ALCOHOL DEHYDROGENASE1)1.280.362.12−0.790.040.38
 AT3G30775ERD5 (PRO OXIDASE)1.270.200.89−0.110.770.75
 AT4G39795Unknown protein; senescence-associated protein-related1.210.522.640.060.030.19
 AT4G17670Unknown protein; senescence-associated protein-related1.060.191.500.210.130.87
 AT5G24660Unknown protein−1.53−0.14−1.42−0.090.02md
 AT5G54770THI1 (THIAZOLE REQUIRING); thiazole biosynthetic enzyme−1.570.05−1.430.250.591.74
 AT1G73120Unknown protein−1.58−0.48−2.670.04−0.06−0.42
 AT2G15620NIR1; ferredoxin-nitrate reductase; ferredoxin-nitrite reductase, putative−1.600.14−0.82−0.45−0.55−1.02
 AT4G19690IRT1; cadmium ion transporter/iron ion transporter (IRT1)−1.61−0.22−2.060.09−0.010.14
 AT1G24280G6PD3; Glc-6-P 1-dehydrogenase ATP-binding−1.63−0.29−1.29−0.32−0.58−1.06
 AT5G07680ANAC079/ANAC080; transcription factor; no apical meristem (NAM) family protein−1.670.22−0.820.090.280.50
 AT5G52790Unknown protein; CBS domain-containing protein-related−1.77−0.37−1.740.130.020.04
 AT3G46900COPT2; copper ion transporter; copper transporter, putative−1.77−0.20−1.390.410.25−0.37
 AT4G34950Unknown protein; nodulin family protein−1.78−0.20−1.06−0.750.591.12
 AT4G02380SAG21 (SENESCENCE-ASSOCIATED GENE21)−1.82−0.10−2.11−1.95−0.08−1.88
 AT4G05230Unknown protein; ubiquitin family protein−1.82−0.38−1.95−0.02−0.25−0.02
 AT1G49500Unknown protein−2.21−0.11−1.80−1.15−2.49−3.61
 AT1G77760NIA1 (NITRATE REDUCTASE1); nitrate reductase 1 (NR1)−2.38−0.11−2.58−0.40−0.60−1.07
 AT4G29905Unknown protein−2.58−0.42−3.450.11−0.74−1.47
Differential expression increased during starvation
 AT5G04120Catalytic; phosphoglycerate/bisphosphoglycerate mutase family protein1.412.533.400.08−0.030.00
 AT5G45380Solute:sodium symporter/urea transporter; sodium:solute symporter family protein3.522.455.200.881.522.62
 AT4G37220Unknown protein; stress-responsive protein, putative0.682.342.04−0.15−0.07−0.65
 AT4G32930Unknown protein GAMMA-VPE; Cys-type endopeptidase/legumain1.161.712.611.372.344.54
 AT1G05250Peroxidase1.121.672.380.00−0.09−0.06
 AT5G63840RSW3 (RADIAL SWELLING3); hydrolase, putative1.291.652.870.010.050.23
 AT1G73220Carbohydrate transporter/transporter1.701.593.610.07−0.080.27
 AT4G32950Catalytic/protein phosphatase type 2C3.961.583.540.12−0.01−0.13
 AT5E22650EUGENE prediction1.121.332.310.06−0.01−0.01
 AT4G33040Electron transporter/thiol-disulfide exchange intermediate; glutaredoxin family protein1.171.112.030.841.742.29
 AT3G48340Cys-type endopeptidase/Cys-type peptidase1.261.092.32−0.120.040.01
 AT5G42610Unknown protein1.391.022.530.160.611.33
 AT1G64590Oxidoreductase; short-chain dehydrogenase/reductase (SDR) family protein1.761.002.09−0.020.070.08
 AT5G60770ATNRT2.4; nitrate transporter; high-affinity nitrate transporter, putative0.970.702.220.08−0.11−0.20
 AT4G12360Lipid binding; protease inhibitor/seed storage/lipid transfer protein (LTP) family protein1.060.640.94−0.050.020.14
 AT5G09220AAP2 (AMINO ACID PERMEASE2); amino  acid permease1.230.582.300.360.812.11
 AT5G01740Unknown protein−1.86−0.61−2.660.09−0.170.14
 AT3G25190Unknown protein; nodulin, putative−1.64−0.63−3.020.24−1.25−1.53
 AT3G07720Unknown protein; kelch repeat-containing protein−1.33−0.63−2.55−0.74−0.85−1.66
 AT2G25450Unknown protein; 2OG-dependent dioxygenase,  putative−1.35−0.70−2.671.050.170.41
 AT1E59250EUGENE prediction−1.49−0.71−1.64−0.27−0.100.11
 AT1G09560GLP5 (GERMIN-LIKE PROTEIN5); nutrient reservoir−1.61−0.75−2.260.17−0.26−0.22
 AT1G01580Ferric-chelate reductase/oxidoreductase;  ferric-chelate reductase, putative−1.99−0.78−2.83−0.05−0.02−0.03
 AT5G10210Unknown protein−1.22−0.80−3.250.62−0.180.70
 AT4G19750Glycosyl hydrolase family 18 protein−1.33−0.89−2.82−0.31−0.19−0.34
 AT2G22122Unknown protein−3.00−0.95−4.65−0.05−0.20−0.03
 AT4G04810Unknown protein; Met sulfoxide reductase  domain-containing protein−1.36−0.99−2.660.050.040.04
 AT4G04830Unknown protein; Met sulfoxide reductase  domain-containing protein−1.38−1.08−3.370.040.150.59
 AT5G23220Catalytic; isochorismatase hydrolase family protein−2.53−1.25−4.250.09−0.02−0.11
 mirspot446aMIR156E−1.44−1.53−2.340.36−2.03−0.99
 AT2G05440Unknown protein; Gly-rich protein−1.76−2.12−5.100.050.09−0.03
Differential expression increased from day 2
 AT1G49320Unknown protein; BURP domain-containing protein0.432.632.170.00−0.170.35
 AT1G12940ATNRT2.5; nitrate transporter; high-affinity nitrate  transporter, putativemd2.544.92−0.030.681.08
 AT3G50970XERO2; dehydrin xero2 (XERO2)/low-temperature- induced protein LTI30 (LTI30)0.211.781.89−0.520.620.08
 mirspot1123aMIR169H0.161.631.720.150.310.54
 AT3G58550Lipid binding; protease inhibitor/seed storage/lipid  transfer protein (LTP) family protein0.391.601.76−0.040.040.28
 AT5G06510Transcription factor; CCAAT-binding transcription  factor family protein0.311.512.200.621.172.46
 AT1G72830HAP2C; transcription factor0.331.492.500.160.610.73
 AT1G73810Unknown protein0.051.412.35−0.210.340.67
 AT1G01380ETC1 (ENHANCER OF TRY AND CPC1); myb  family transcription factor−0.041.322.13−0.01−0.050.15
 AT1G54575Unknown protein0.651.252.010.161.102.47
 AT1G21890Unknown protein; nodulin MtN21 family protein−0.071.212.79−0.010.050.32
 AT3G05690HAP2B; transcription factor0.150.921.820.081.081.76
 mirspot1002MIR160C0.470.722.00−0.320.501.62
 mirspot690aMIR8360.180.701.930.06−0.07−0.10
 AT3G21420Oxidoreductase; oxidoreductase, 2OG-Fe(II)  oxygenase family protein0.640.691.840.04−0.020.31
 AT3G58990Hydrolyase; aconitase C-terminal domain- containing protein−0.66−0.61−1.44−0.51−1.55−2.17
 AT3G18080Hydrolase, hydrolyzing O-glycosyl compounds;  glycosyl hydrolase family 1 protein−0.65−0.62−1.76−0.03−0.040.05
 AT5G10180AST68; sulfate transporter−0.56−0.66−1.67−0.17−0.84−1.66
 AT2G36120Unknown protein; pseudogene, Gly-rich protein−0.61−0.69−2.51−0.21−0.58−1.40
 AT2G36830GAMMA-TIP; water channel; major intrinsic  family protein/MIP family protein−0.55−0.72−1.87−0.85−1.12−2.96
 AT5G23020MAM-L (METHYLTHIOALKYMALATE  SYNTHASE-LIKE); 2-isopropylmalate synthase 2−0.54−0.74−1.90−0.10−1.03−0.39
 AT3G61430PIP1A; water channel; plasma membrane intrinsic  protein 1A−0.41−0.78−2.00−0.05−0.87−1.46
 AT4G01470GAMMA-TIP3/TIP1;3; water channel; major  intrinsic family protein/MIP family protein−0.39−0.84−1.780.090.220.23
 AT3G02885GASA5; gibberellin-regulated protein 5 (GASA5)/ gibberellin-responsive protein 5−0.59−0.85−1.790.17−0.09−1.16
 AT2G33790Unknown protein; pollen Ole e 1 allergen and  extensin family protein0.01−0.87−1.97−0.090.080.23
 AT4G17340DELTA-TIP2/TIP2;2; water channel; major intrinsic  family protein/MIP family protein−0.25−0.97−2.300.01−0.020.08
 AT5G47450AtTIP2;3; water channel; major intrinsic family  protein/MIP family protein−0.23−0.98−2.370.05−0.02−0.04
 AT1G48750Lipid-binding clathrin-binding−0.54−1.24−2.620.13−0.100.42
 AT3G05950Nutrient reservoir; germin-like protein, putative−0.10−2.10−3.77−0.07−0.07−0.05
 AT4G25100FSD1 (FE SUPEROXIDE DISMUTASE1)−0.37−2.33−2.230.14−1.020.15
  • a Identifiers corresponding to genes encoding precursors of known or predicted new small RNA are listed as shown on the Flagdb++ Web site (http://urgv.evry.inra.fr/projects/FLAGdb++/HTML/index.shtml; http://urgv.evry.inra.fr/CATdb).