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Table 1 Over-represented GO groups and promoter consensus sequences

From: Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae

Cluster GO group
Cluster 1 Metabolism
  Biosynthesis
  Cell organization and biogenesis
  Amino acid metabolism
  Nucleotide metabolism
  Protein metabolism
  Nucleotide biosynthesis
  Carboxylic acid metabolism
  tRNA modification
  Ribosome biogenesis and assembly
  Nucleobase, nucleoside, nucleotide, and nucleic acid metabolism
  Glutamate biosynthesis
  TGAAAA/TTTTCA
  GAAAAA/TTTTTC
Cluster 2 Cell growth and/or maintenance
  Mitotic cell cycle
  Physiologic process
  Nuclear organization and biogenesis
  Organelle organization and biogenesis
  Cytoplasm organization and biogenesis
  Cytoskeleton organization and biogenesis
  Morphogenesis
  Reproduction
  AAATTT/AAATTT
  GAAAAA/TTTTTC
Cluster 3 Ribosome biogenesis
  Cytoplasm organization and biogenesis
  RNA metabolism
  Aerobic respiration
  Nucleobase, nucleoside, nucleotide, and nucleic acid metabolism
  Cell growth and/or maintenance
  AATTCA/TGAATT
Cluster 4 Lipid metabolism
  Steroid metabolism
  Amino acid biosynthesis
  Glutamine family amino acid biosynthesis
  Cell growth and/or maintenance
  Arginine biosynthesis
  ATAACA/TGTTAT
Cluster 5 Cell growth and/or maintenance
  Protein modification
  Protein amino acid phosphorylation
  Organelle organisation and biogenesis
  Cell wall organization and biogenesis
  Cell organization and biogenesis
  Signal transduction
  Cytokinesis
  Amino acid biosynthesis
Cluster 6 DNA replication and chromosome cycle
Cluster 7 -
Cluster 8 Transport
  GAAAAA/TTTTTC
Cluster 9 Steroid metabolism
  Alcohol metabolism
  Ergosterol biosynthesis
  Ammonium transport
  Biological process unknown
Cluster 10 Carboxylic acid metabolism
  Sporulation
  Nitrogen utilization
  Carnitine metabolism
  Main pathways of carbohydrate metabolism
  Energy pathways
  Sporulation
Cluster 11 RNA splicing
  mRNA metabolism
  Regulation of transcription
Cluster 12 Meiosis
  Meiotic prophase I
  Nuclear division
  Response to stimulus
  AAGGGG/CCCCTT
Cluster 13 Autophagy
  Vitamin metabolism
  Fatty acid β-oxidation
  Response to water
  Biological process unknown
  AAGGGG/CCCCTT
  AGGGAG/CTCCCT
  AAAAGG/CCTTTT
  AAAGGG/CCCTTT
  AGGGGG/CCCCCT
  1. Shown are over-represented GO [61,62] groups and promoter consensus sequences in the 13 clusters of growth regulated genes. GO groups describing a cellular process with P < 10-4 were considered significant and included in the table. If the same set of genes was found in two or more neighbouring GO groups, only one GO term is included [63]. Hexamers, found in the 800 base pair upstream region of ORFs in a cluster, were considered significantly over-represented when E < 10-2 [64,65]. GO, Gene Ontology; ORF, open reading frame.