Appendix S1. List of all significantly differentially expressed SAGE tags

Gene Identified / SAGE Tag
Functional Category / Gene / Rank / Tag Sequence / Base Count / Crown Count / P Value
Crown-Abundant Genes
1. Cell Wall / A. Basic Carbohydrate Metabolism / Fructokinase F28G11.11 [Imported](Putative) / 366 / AGAATCGCTA / 13 / 26 / 0.009
GAP Dehydrogenase / 55 / GCTTTAGTTG / 74 / 113 / 0.000
Glucose-6-Phosphate/Phosphate-Translocator Protein / 57 / AACTACTATG / 5 / 24 / 0.000
NADP-Isocitrate Dehydrogenase / 223 / GGTATCCGTT / 4 / 15 / 0.004
B. Nucleotide Sugar Metabolism / Alpha-1,4-Glucan-Protein Synthase (UDP-Forming Enzyme) / 260 / CTCAACAGAG / 14 / 29 / 0.004
Epimerase/Dehydratase Family Protein (NAD-Dependent) / 39 / GTTGATGGCC / 13 / 42 / 0.000
Exostosin Family / 381 / GCTGTTGTTC / 0 / 8 / 0.009
UDP-Glucoronosyl/UDP-Glucosyl Transferase Family Protein / 15 / GTGAATCTGC / 32 / 85 / 0.000
UDP-Glucose Dehydrogenase (EC 1.1.1.22) / 142 / GGAATGGGTT / 69 / 97 / 0.001
UDP-N-Acetylglucosamine 1-Carboxyvinyltransfe / 184 / AAAGGATCCA / 0 / 8 / 0.002
C. Polymerization / Cellulose Synthase-4 / 195 / TCTGCGGAAT / 12 / 28 / 0.002
Glucan Synthase (Putative) / 117 / CCCACTGGAT / 5 / 20 / 0.001
Pectin Methyl Esterase (EC 3.1.1.11) / 104 / CAATCGTACA / 38 / 64 / 0.001
Pectinesterase Like Protein / 96 / GACAGCTATT / 0 / 17 / 0.000
D. Catabolism / Beta-1,4-Glucanase (Endo) / 53 / TGTTCGAACT / 48 / 83 / 0.000
Glycosyl Hydrolase Family 5/Cellulase / 51 / TTCCAAGCTG / 0 / 14 / 0.000
E. other / Dihydrolipoamide Succinyltransferase -Related / 280 / CTGTTTCATT / 5 / 16 / 0.005
Sugar Transporter-Like Protein / 79 / TTCACCATTG / 12 / 33 / 0.000
F. Lignin Amino Acid Metabolism / Acetylornithine Aminotransferase / 376 / CATTCTGGCT / 0 / 8 / 0.009
Glutamine synthetase (EC 6.3.1.2) / 163 / ACTCTGATAT / 66 / 93 / 0.001
Glycine Hydroxymethyltransferase (EC 2.1.2.1) / 182 / GGAAGCTTCT / 60 / 85 / 0.002
Methionine Synthase / 11 / TGCTACTCTA / 31 / 103 / 0.000
Methionine Synthase / 31 / GTTGCATCTG / 44 / 88 / 0.000
Methionine Synthase (Cobalamine Independent) / 29 / GTTGCAGCTG / 108 / 167 / 0.000
Phosphoserine Aminotransferase, Chloroplast Precursor / 272 / CGTTCTGCAC / 9 / 22 / 0.005
G. Lignin SAM Metabolism / SAM Decarboxylase / 40 / TCAGTCAGAA / 66 / 110 / 0.000
SAM Synthetase / 59 / ATTTCTATCA / 4 / 22 / 0.000
SAM Synthetase (EC 2.5.1.6) / 175 / GAGGAGGGGC / 10 / 26 / 0.001
SAM Synthetase 1 / 35 / ATCACGATCA / 82 / 132 / 0.000
SAM Synthetase 2 / 7 / ATGACTATCA / 52 / 138 / 0.000
H. Lignin Other / 4-Coumarate-Coa Ligase (EC 6.2.1.12) 4CL2 / 124 / ACAGAAGCAG / 30 / 54 / 0.001
Laccase / 9 / GTGTTTGTGG / 71 / 127 / 0.000
Laccase / 74 / ATCACAGCAA / 18 / 42 / 0.000
Phenylcoumaran Benzylic Ether Reductase (PCBER) / 215 / GTTCTATTTT / 5 / 17 / 0.003
Pinoresinol-Lariciresinol Reductase / 157 / TTATGGAGCC / 9 / 25 / 0.001
I. Cell Wall Loosening / Expansin-Like Protein / 362 / ACTGTGAAAG / 5 / 15 / 0.009
Xyloglucan Endotransglycosylase / 22 / TAACACAATC / 10 / 51 / 0.000
Xyloglucan Endotransglycosylase Precursor / 198 / ACTATTGGGG / 10 / 25 / 0.002
J. CW Structural / Arabinogalactan Protein (Putative) / 25 / AAGCAGAAGA / 6 / 41 / 0.000
Arabinogalactan Protein (Putative) / 299 / GAGAAGATGG / 23 / 39 / 0.007
Arabinogalactan Protein (Putative) / 383 / GGTCTTTCTC / 0 / 8 / 0.009
K. Cytoskeleton / Actin (Imported) / 98 / AAAATCAAGG / 51 / 80 / 0.000
Actin Depolymerising Factor (Putative) / 75 / TAGCATCTCT / 95 / 132 / 0.000
Alpha Tubulin / 1 / TATGCCAAGC / 188 / 298 / 0.000
Alpha Tubulin / 282 / GTATCTGATA / 78 / 100 / 0.005
Calcium Binding Protein (Putative) / 109 / GTAAGCTTGA / 0 / 10 / 0.001
Calcium Binding Protein CCD1 / 154 / GCTTCCAGTT / 9 / 25 / 0.001
Calcium-Binding Protein / 114 / TTAAGCTTGA / 0 / 10 / 0.001
Calmodulin / 61 / ACAAATTTAG / 45 / 78 / 0.000
Calmodulin [Imported] (Putative) / 270 / CCAAGAGGGT / 34 / 53 / 0.005
Tubulin Beta-3 Chain (Beta-3 Tubulin) / 227 / TACTTTTCTG / 13 / 28 / 0.004
2. Electron Transport / Blue Copper Protein / 19 / AATGAGATGC / 0 / 61 / 0.000
Blue Copper Protein (Basic) / 10 / GACTACTGGG / 60 / 114 / 0.000
Blue Copper Protein, Putative / 179 / GAATCTCAAA / 16 / 34 / 0.002
Ubiquinol--Cytochrome-C Reductase (Putative) / 141 / CAAGTGGATT / 6 / 21 / 0.001
3. Energy / Adenosine Kinase-Like Protein (Fragment) / 86 / CAGCTCAGAA / 17 / 39 / 0.000
ADP,ATP Carrier Protein F20O9.60 / 105 / ACTCTGGCTC / 58 / 87 / 0.001
ATP Synthase Epsilon Subunit / 37 / CTCAGAGGTT / 6 / 31 / 0.000
ATPase (P-type H+-) / 67 / GTTTGCATAC / 4 / 21 / 0.000
ATPase Subunit C (Vacuolar) / 49 / GCTGGAGTGT / 45 / 81 / 0.000
Proton-Inorganic Pyrophosphatase (Vacuolar) / 70 / AAATATAAAC / 31 / 59 / 0.000
UMP/CMP Kinase b (EC 2.7.1.48) / 85 / AAAGTGAGAA / 14 / 35 / 0.000
4. Membrane / Aquaporin Like Protein / 8 / CCGTTTGTGA / 67 / 128 / 0.000
Calreticulin / 12 / ACGAGTTGTA / 34 / 93 / 0.000
Lipid Transfer Protein / 13 / AAGCTGCCTG / 26 / 89 / 0.000
Plasma Membrane Associated Protein (Putative) / 301 / AAAAATCAGA / 0 / 6 / 0.008
Porin MIP 1 / 4 / TGTATTGTTG / 115 / 191 / 0.000
Vesicle Trafficking Protein (Putative) / 372 / AACCTTCAAG / 0 / 8 / 0.009
5. Metabolism / Beta 2 Subunit Of 20S Proteasome / 353 / CCTAATGAAA / 3 / 12 / 0.008
Cationic Peroxidase 1 Precursor (EC 1.11.1.7) / 327 / GTGAAAATGG / 0 / 6 / 0.008
Cysteine Proteinase / 56 / CAAGCTTCAT / 17 / 43 / 0.000
Cystien Proteinase Inhibitor / 62 / CATCTGAATG / 36 / 67 / 0.000
Histidine-Containing Phosphotransfer Protein / 205 / ATGTCGGCTT / 3 / 14 / 0.002
Lipase, (Probable) (Imported) / 54 / AGGGAATGGC / 19 / 46 / 0.000
Sphingolipid Long Chain Base Delta 8 Desaturase / 119 / TCCAAGCCTA / 5 / 20 / 0.001
Superoxide Dismutase (Cu-Zn) (EC 1.15.1.1) / 100 / AACTGAGTAA / 35 / 61 / 0.000
Ubiquitin Conjugating Enzyme (Putative) / 345 / ATACCTATGT / 9 / 21 / 0.008
6. Other / Defender Against Cell Death 1 (DAD-1) / 258 / CTCAAGAAGC / 17 / 33 / 0.004
Annexin (Fragment) / 196 / TTTGCTACCA / 4 / 16 / 0.002
Asparagus SHH [unidentified] / 361 / TTATGAATCA / 134 / 154 / 0.009
CCR4-Associated Factor (Putative) / 87 / GGGGATTGAA / 5 / 21 / 0.000
EDS1-Like Protein / 365 / TTCAATCCAA / 5 / 15 / 0.009
Erg-1 / 371 / AAATTTTCCC / 0 / 8 / 0.009
Ftsk/Spoiiie Family Protein / 289 / ATAGGTACTG / 27 / 44 / 0.006
GTP-Binding Nuclear Protein RAN-A1 / 122 / TTTGATGTTA / 25 / 48 / 0.001
Hairpin Induced Family Protein / 42 / GCTCTGTTGA / 87 / 133 / 0.000
Histone H1 (Putative) / 292 / GCTTCCACTG / 8 / 20 / 0.006
Histone H3.3 / 271 / CAATGCATAA / 9 / 22 / 0.005
LIM Domain Protein WLIM-1 / 199 / GATGTAGGAT / 34 / 55 / 0.002
Luminal Binding Protein / 392 / TTGAAATCAT / 0 / 8 / 0.009
Luminal Binding Protein 3 (BIP 3) / 89 / AAAAACACAA / 4 / 19 / 0.000
MADS Box Protein MADS8 (Putative) / 152 / TGCATTGAAG / 0 / 9 / 0.001
MADS-Box Protein MADS9 / 235 / ATATCTGCAA / 0 / 7 / 0.004
Mitochondrial Dicarboxylate Carrier (Putative) / 204 / AGTTCAAGTC / 3 / 14 / 0.002
Nonclathrin Coat Protein Zeta2-COP / 394 / TTTTGTGTTT / 0 / 8 / 0.009
Peptidyl-Prolyl Cis-Trans Isomerase, (Putative) / 330 / GTTGGATAAA / 0 / 6 / 0.008
Putative Retroelement (Putative Gag-Pol Polyprotein) / 234 / ATATAAATAA / 0 / 7 / 0.004
Syringolide-Induced Protein 19-1-5 / 262 / TACCCCTGTG / 27 / 45 / 0.004
7. Ribosomal Proteins / 40S Ribosomal Protein S18 / 97 / AGGCTCAGAG / 9 / 27 / 0.000
40S Ribosomal Protein S8 / 216 / AGGGAATTTA / 18 / 35 / 0.003
40S Ribosomal Protein S9 / 369 / AAGGCAGCCT / 47 / 65 / 0.009
60S Ribosomal Protein L10 (Wilm's Tumor Suppressor Homolog) / 259 / GATCTGTCTC / 62 / 84 / 0.004
60S Ribosomal Protein L12 / 153 / CCTCTCCGTC / 9 / 25 / 0.001
60S Ribosomal Protein L15-2 / 364 / GAAGAAAAAC / 5 / 15 / 0.009
Acidic Ribosomal Protein P1a / 139 / GGATTCAGCT / 82 / 112 / 0.001
Ribosomal Protein L19 (Putative) / 41 / AAAGTCAAGG / 10 / 36 / 0.000
Ribosomal Protein L6 / 18 / AGCTTGCTTT / 19 / 65 / 0.000
Ribosomal Protein S19 / 44 / GCTTGATTAG / 17 / 46 / 0.000
Ribosomal Protein S2, Cytosolic (Similarity) / 121 / CCTGTGCAGA / 25 / 48 / 0.001
Ribosomal Protein S20, Cytosolic / 140 / AGCATTCAAA / 6 / 21 / 0.001
Ribosomal Protein S27 / 283 / GATGTAAAGT / 25 / 42 / 0.005
Ribosomal Protein S4 / 17 / TGCAAGATGC / 27 / 70 / 0.000
S28 Ribosomal Protein / 395 / CAAGGCACTA / 69 / 88 / 0.010
8. Signal Transduction / Abscisic Acid-Induced Protein-Rice (Putative) / 115 / CCAGACTGTT / 5 / 20 / 0.001
Auxin-Induced Protein (Clone MII-3) / 68 / TTGTGGCCAA / 25 / 52 / 0.000
Cyclophilin / 36 / ACTCCCTAGG / 52 / 96 / 0.000
Phosphate Responsive Protein / 21 / ATCATCAACA / 8 / 53 / 0.000
Receptor-Protein Kinase (Putative) / 391 / TTACAGGCAG / 0 / 8 / 0.009
9. Stress Response Realted / Chitinase-1(Bulb) / 77 / ATTGCTACTT / 19 / 43 / 0.000
Dehydrin / 82 / TATATGAGAG / 6 / 23 / 0.000
Dehydrin / 293 / TTATGGTTTG / 18 / 33 / 0.007
Dehydrin (Putative) / 168 / GTCACGAGGG / 70 / 97 / 0.001
Dehydrin (Putative) / 370 / GGGGTGAAGA / 48 / 66 / 0.009
GRP 94 / 129 / GAATTTAGGA / 0 / 12 / 0.001
Heat Shock Protein 70 / 47 / AGGAATACCA / 40 / 75 / 0.000
Heat Shock Protein 81-2 / 50 / GATGAGCTTA / 31 / 63 / 0.000
10. Transcription and Translation / DNA Binding Protein / 5 / TGTAACAGCC / 86 / 180 / 0.000
Glycine Rich RNA Binding Protein / 6 / GTCTACTGAC / 45 / 150 / 0.000
Glycine-Rich RNA-Binding Protein / 300 / GTTATGGTTT / 64 / 84 / 0.007
RNA Binding Protein / 76 / CAACTGATTT / 42 / 72 / 0.000
RNA Binding Protein (Putative) / 207 / GTACAGTTCT / 0 / 14 / 0.002
RNA-Binding Like Protein (Imported) / 73 / CTTCACCATT / 0 / 12 / 0.000
Transcription Initiation Factor IIA Gamma Cha / 339 / TTATTCGTAG / 0 / 6 / 0.008
Translation Factor (Putative) / 229 / CATCTTCGTA / 8 / 21 / 0.004
Translation Initiation Factor eIF-1A (Probable) / 202 / TTTGAGTTTT / 8 / 22 / 0.002
Translation Initiation Factor Eif-4A.15 / 217 / TTCCATTTTG / 12 / 27 / 0.003
Zinc Finger Protein (Putative) / 183 / ACAGCAAGTG / 9 / 24 / 0.002
Base-Abundant Genes
1. Cell Wall / A. Basic Carbohydrate Metabolism / Fructose-Bisphosphate Aldolase (EC 4.1.2.13) / 56 / GATTAGTTTT / 132 / 96 / 0.000
C. Polymerization / Pectinesterase Homolog / 74 / GTCACCGGCC / 16 / 3 / 0.001
D. Catabolism / Beta-1,3-Glucanase-Like Protein / 55 / TCTTTCATTT / 12 / 1 / 0.000
E. other / Lectin Like Protein / 18 / GAAGATCGAT / 42 / 12 / 0.000
H. Lignin Other / Laccase / 105 / AATAAAAGAG / 23 / 8 / 0.001
SAM Synthetase (EC 2.5.1.6) / 94 / GGTTTCACAT / 17 / 4 / 0.001
J. CW Structural / Arabinogalactan Like Protein / 271 / CATTCATTCT / 8 / 1 / 0.009
Arabinogalactan protein (Putative) / 151 / CTGGTATGCC / 12 / 2 / 0.003
Arabinogalactan protein (Putative) / 252 / TTTTCCTATT / 137 / 117 / 0.009
Arabinogalactan/Proline-Rich Protein (Putative) / 195 / TTTCTAGTTA / 44 / 27 / 0.006
Arabinogalactan-Like Protein / 96 / GCGGCCCTGG / 227 / 197 / 0.001
Proline Rich Protein / 54 / ATGGGGAAAT / 12 / 1 / 0.000
Proline-Rich Protein / 95 / CAGTGATTTT / 82 / 56 / 0.001
Proline-Rich Protein / 76 / TAACGACAGT / 30 / 12 / 0.001
K. Cytoskeleton / Actin (Imported) / 69 / TTATAATATC / 74 / 47 / 0.001
Calcium Binding Protein / 230 / TACTCTTTCT / 6 / 1 / 0.008
Calmodulin / 107 / CTGCAATGTT / 43 / 23 / 0.002
Microtubule Associated Protein / 138 / CTGCCAGTGT / 22 / 8 / 0.002
Profilin / 109 / TATGTTTGCC / 93 / 67 / 0.002
Tubulin Beta-2 Chain / 197 / CAGTACCAGG / 14 / 4 / 0.006
2. Electron Transport / Blue Copper Protein, Putative / 200 / TATACATTAC / 112 / 91 / 0.007
Cytochrome P450 90A1 / 276 / GAGATGGGAA / 8 / 1 / 0.009
Thioredoxin H-type (TRX-H) / 43 / CTGCAAATGG / 122 / 84 / 0.000
3. Hormone / Auxin Repressed Protein Like Protein / 4 / GCGGTAGTGG / 112 / 46 / 0.000
Auxin-Repressed Protein Like Protein / 270 / CAGTATGTAT / 8 / 1 / 0.009
Ethylene Forming Enzyme (Putative) / 101 / CTTTTTGACA / 13 / 2 / 0.001
4. Membrane / Core Protein / 253 / CAGTACCTAG / 31 / 17 / 0.009
Non Specific Lipid Transfer Protein / 8 / GGAATGCCTT / 114 / 35 / 0.000
Phytocyanin Homolog / 59 / GATTCTGTAA / 16 / 2 / 0.000
Phytocyanin Homolog / 136 / GTTGGATCAT / 53 / 32 / 0.002
Potassium Channel Beta Subunit / 37 / GCGCCCATCT / 32 / 10 / 0.000
Secretory Protein-Like / 46 / GTCCACCTGT / 31 / 10 / 0.000
Tonoplast Intrinsic Protein, Delta Type / 2 / AACCCGGCCC / 134 / 76 / 0.000
5. Metabolism / Acid Phosphatase (Putative) (Fragment) / 166 / GGAAGAAATT / 52 / 33 / 0.004
Golgi SNARE 12 Protein / 154 / TATTTTGTTA / 12 / 2 / 0.003
S-Like Ribonuclease (RNase PD2) (Fragment) / 90 / GTTGTGTTTC / 25 / 9 / 0.001
Ubiquitin Conjugating Protein (EC 6.3.2.19) / 201 / TAATCTTCCC / 56 / 38 / 0.007
Ubiquitin-Like Protein SMT3-like / 194 / TTTTTCAACT / 23 / 10 / 0.006
Vacuolar Proton Inorganic Pyrophosphatase / 23 / AAAAATGGCA / 16 / 1 / 0.000
6. Other / Copia Like Reteroelement / 26 / GTAATTCAGT / 30 / 7 / 0.000
Csf-1 Protein (Fragment) / 196 / CACGCATTTT / 14 / 4 / 0.006
Delta-COP / 171 / GCCTTTGGTT / 22 / 9 / 0.005
GASA5-Like Protein [Imported] / 77 / TATTTATATA / 21 / 6 / 0.001
Nicotinamine Synthase / 11 / GCCCCCGGTG / 52 / 13 / 0.000
Nucleoid DNA-Binding Protein Cnd41-Like Protein / 116 / GCCATCGGCT / 36 / 18 / 0.002
Phosphate Transport Protein, Mitochondrial / 92 / ATAATAAAAA / 45 / 24 / 0.001
Photoassimilate-Responsive Protein PAR-like Protein / 52 / GGCAGAGTGA / 167 / 127 / 0.000
7. Ribosomal Proteins / 40S Ribosomal Protein S30 / 172 / GTTCCCTTGC / 22 / 9 / 0.005
60s Acidic Ribosomal Protein / 50 / GCGTACATCG / 162 / 122 / 0.000
60S Ribosomal Protein (Putative) / 157 / GCAAACCATT / 45 / 26 / 0.003
60S Ribosomal Protein L18a / 115 / AACTTCAGAG / 77 / 53 / 0.002
60S Ribosomal Protein L24 / 188 / CTGAACAAGT / 16 / 5 / 0.005
60S Ribosomal Protein L36 (Putative) / 173 / GCGCCTGCGC / 30 / 15 / 0.005