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Table 1 Total number of changed stem transcripts in three major functional categories of B. napus DH12075 (DH) and YN01–429 (YN)

From: Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content

  DH4:YN4 DH1:YN1 DH1:DH4 YN1:YN4
Up Down Up Down Up Down Up Down
Cellular Component
 Other intracellular components 754 693 668 580 475 396 377 205
 Chloroplast 602 567 581 462 413 320 308 159
 Other cytoplasmic components 636 469 531 403 361 321 280 161
 Other membranes 531 482 466 483 374 290 284 156
 Unknown cellular components 607 607 513 373 463 352 347 187
 Plastid 291 343 260 303 174 151 246 122
 Plasma membrane 438 381 421 326 262 240 133 79
 Nucleus 392 227 331 200 247 203 181 107
 Other cellular components 284 285 184 153 225 162 163 103
 Mitochondria 198 191 210 188 125 94 97 55
 Cell wall 127 123 115 88 75 66 64 40
 Cytosol 121 102 106 80 66 66 56 31
 Extracellular 110 82 82 62 66 62 44 33
 ER 90 76 81 60 60 48 44 33
 Golgi apparatus 49 43 40 37 31 26 18 12
 Ribosome 23 23 23 18 16 13 10 8
Molecular Function
 Other enzyme activity 515 695 439 383 492 295 383 216
 Unknown molecular functions 650 471 578 515 341 376 259 156
 Other binding 525 469 455 393 327 274 248 150
 Transferase activity 295 308 243 229 211 186 188 100
 Hydrolase activity 341 328 275 299 240 199 151 98
 Protein binding 351 260 306 230 223 199 176 115
 Nucleotide binding 279 132 231 217 131 96 139 53
 Kinase activity 137 245 114 110 175 143 85 88
 DNA or RNA binding 257 182 160 183 83 125 121 73
 Transporter activity 164 201 197 131 153 93 70 56
 Other molecular functions 185 157 143 110 122 93 103 45
 Transcription factor activity 165 149 130 115 117 93 79 47
 Nucleic acid binding 119 111 98 102 76 64 61 28
 Structural molecule activity 35 22 28 25 26 16 20 8
 Receptor binding or activity 15 18 17 12 16 10 9 5
Biological Process
 Other cellular processes 1254 1145 1066 943 803 710 641 398
 Other metabolic processes 1139 1016 974 860 754 664 597 364
 Unknown biological processes 763 760 637 575 583 418 444 233
 Response to abiotic or biotic stimulus 387 373 350 279 221 197 200 115
 Response to stress 381 342 337 263 206 188 181 115
 Other biological processes 353 334 325 269 215 197 183 105
 Protein metabolism 375 359 333 317 247 229 130 127
 Developmental processes 251 261 222 181 197 158 189 83
 Transport 266 232 232 193 165 124 139 85
 Cell organization and biogenesis 171 154 150 137 127 110 97 56
 Transcription 159 146 130 119 104 88 73 42
 Electron transport or energy pathways 81 74 61 54 51 31 45 17
 Signal transduction 75 52 66 46 39 38 37 22
 DNA or RNA metabolism 35 27 24 21 25 20 18 14
  1. NB data was ranked in descending order using the DH4-YN4 pair wise comparison. Up., upregulated. Down, down regulated