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Table 1 GO categorization of differentially expressed poplar genes during in vitro organogenesis

From: Genome scale transcriptome analysis of shoot organogenesis in Populus

   B vs. A C vs. A D vs. A E vs. A
GO category Function category Up Down Up Down Up Down Up Down
Biological Process response to stress 1.8 1.8 2.1 1.7 2.3 1.6 2.3 1.8
  cell organization and biogenesis 1.6 1.2 1.1 1.2 1 1.3 1 1.3
  response to abiotic or biotic stimulus 1.5 2 1.8 2 1.9 1.8 1.8 1.9
  developmental processes 1.5 1.3 1.4 1.4 1.3 1.6 1.5 1.6
  other metabolic processes 1.3 1.2 1.3 1.2 1.4 1.1 1.4 1.1
  other cellular processes 1.3 1.2 1.3 1.2 1.3 1.2 1.3 1.1
  protein metabolism 1.3 1 1 1 1 1 1 1
  electron transport or energy pathways 1.2 1.8 1.5 1.7 1.6 1 1.6 1.1
  transport 1.1 1.2 1.1 1.2 1.1 1.4 1.1 1.3
  DNA or RNA metabolism 1.1 0.4 0.6 0.5 0.6 0.6 0.6 0.6
  other biological processes 0.9 0.9 0.9 0.9 0.9 1 0.9 1
  signal transduction 0.9 1.4 1 1.4 1.1 1.6 0.9 1.8
  transcription 0.8 1.1 1 1.1 1 1.3 1 1.4
Cellular Component ribosome 2.8 0.9 0.9 1 1.1 0.2 1.5 0.2
  cytosol 2.8 1.1 2.1 1.1 2.3 0.9 2.8 1
  mitochondria 2.6 0.9 1.9 0.8 1.9 0.8 1.8 0.7
  cell wall 2.2 0.9 2 1.2 2.1 1.3 2.5 1.3
  other cytoplasmic components 2 2.1 1.4 1.9 1.5 1.2 1.6 1
  ER 2 0.2 2.1 0.5 2.1 0.8 2.4 0.4
  other intracellular components 1.6 1.6 1 1.4 1 1.1 1.1 1
  Golgi apparatus 1.3 1.2 0.7 1.5 0.7 2 0.4 1.8
  nucleus 1.1 1.1 1.2 1.1 1 1.3 1 1.3
  plasma membrane 1.1 1.9 1.3 2.3 1.4 2.5 1.1 2.6
  other cellular components 1 1 0.9 0.9 0.9 0.9 0.9 0.9
  chloroplast 1 2.5 0.9 2.1 1 1.2 1.1 1.2
  other membranes 0.9 1.2 1.1 1.3 1.2 1.2 1.1 1.1
  plastid 0.9 4.9 0.9 3.9 1 1.4 1.1 1.2
  extracellular 0.8 0.6 1.1 0.8 1.2 0.7 1.4 0.5
Molecular Function structural molecule activity 2.2 1.4 0.7 1.3 0.9 0.8 1.2 0.8
  other enzyme activity 1.8 1.3 2 1.3 2.2 1 2.2 1
  nucleotide binding 1.7 0.9 1.4 1.1 1.3 1.2 1.2 1.2
  nucleic acid binding 1.6 0.9 1.2 0.9 0.9 0.9 1 0.9
  transferase activity 1.5 1.2 1.9 1.2 1.8 1.3 1.9 1.3
  transporter activity 1.4 1.3 1.4 1.4 1.4 1.6 1.4 1.6
  hydrolase activity 1.4 1.1 1.3 1.2 1.2 1.1 1.4 1.1
  kinase activity 1.1 1.3 1.4 1.4 1.4 1.7 1.2 1.8
  DNA or RNA binding 1 1 0.9 0.9 0.9 1 0.8 1.1
  protein binding 1 1.3 1 1.3 0.9 1.5 0.8 1.6
  transcription factor activity 0.8 1.4 1 1.5 1.1 1.7 1.1 1.8
  other binding 0.8 1 0.8 0.9 0.8 0.9 0.7 0.9
  other molecular functions 0.7 0.8 0.7 0.8 0.7 0.8 0.6 0.8
  receptor binding or activity 0.5 0.7 0.7 0.6 0.6 0.6 0.6 0.7
  1. The Arabidopsis homologs of the identified differentially expressed poplar gene were used for GO categorization. The percentage of each functional class in the poplar genome is assumed to equal to that in Arabidopsis.