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Table 3 Selected GO biological process terms over- and underrepresented among genes called up and down.

From: Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana

sample GO term no. (%) in sample no. (%) in all genes P-value
bold = underrepresented
all genes in experiment
n = 11,091 annotated
    
2xX4x down
n = 71 annotated
response to stimulus 15(21.12) 817(7.3) 0.00159
  regulation of transcription, DNA-dependent 8(11.26) 374(3.37) 0.0181
2xX6x up
n = 228 annotated
cell wall organization and biogenesis 8 (3.5) 80 (0.72) 0.0371
  inorganic anion transport 4(1.75) 20(0.18) 0.0483
2xX6x down
n = 302 annotated
microtubule-based movement 9(2.98) 26(0.23) 2.56 e-06
  regulation of cell cycle 7(2.31) 38(0.34) 0.00426
  steroid metabolic process 4(1.32) 18(0.16) 0.0373
fis1X2x up
n = 304 annotated
carbohydrate metabolic process 27(8.88) 351(3.16) 7.88 e-06
fis1x2x down
n = 541 annotated
biosynthetic process 16(2.77) 773(6.96) 0.0342
  electron transport 33(6.09) 352(3.17) 0.0295
  regulation of biological process 63(11.64) 838(7.55) 0.0342
  regulation of cell cycle 8(1.47) 38(0.34) 0.0345
  sequestering of lipid 4(0.73) 8(0.72) 0.0342
  response to chemical stimulus 31(5.73) 348(3.13) 0.0399
4x X 2x up
n = 219 annotated
cellular process 44(20.09) 3665(33.0) 0.0141
6xX2x up
n = 554 annotated
defense response 30(5.41) 189(1.70) 8.11 e-09
  response to stimulus 67(12.09) 817(7.36) 0.00345
  response to starvation 5(0.9) 14(0.13) 0.019
  macromolecule metabolic process 73(13.17) 2300(20.74) 0.00246
6xX2x down
n = 697 annotated
translation 41(5.88) 276(2.49) 2,76 e-06
  macromolecule biosynthetic process 48(6.88) 380(3.42) 5.57 e-05
  macromolecule metabolic process 185(26.54) 2300(20.73) 0.00551
  DNA replication initiation 4(0.57) 7(0.06) 0.0207
  transcription factor import into nucleus 3(0.43) 4(0.04) 0.0367
  DNA metabolic process 29(4.16) 168(1.5) 2.76 e-06
  nucleosome assembly 11(1.57) 28(0.25) 5.57 e-05
  chromatin assembly and disassembly 12(1.72) 38(0.34) 0.00019
  organelle organization and biogenesis 42(6.02) 291(2.62) 2.76 e-06
  cellular component organization and biogenesis 63(9.03) 618(5.57) 0.00282
  microtubule-based movement 7(1.0) 26(0.23) 0.0358
  1. The GOstat tool (http://gostat.wehi.edu.au/; Beissbarth and Speed, 2004) was used to identify GO biological process terms significantly (P < 0.05) over- and underrepresented among genes called up and down. P-values were adjusted using the Benjamini and Hochberg correction for multiple testing. Each list was compared with the set of all genes called present in the experiment.
  2. n = number of genes in each list with GO biological process annotation.