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Table 1 Details of the behaviors of the 41 duplicated pairs present in the PRODISTIN classification tree

From: A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network

Behavior class Gene 1 Gene 2 Localization in same PRODSTIN class Same cellular function Annotation of the PRODISTIN classes by cellular function
I ARF1 ARF2 + + Vesicle-mediated transport, secretory pathway, intracellular transport (50)
  ASM4 NUP53 + + Nuclear organization and biogenesis (22), nucleobase nucleoside nucleotide and nucleic acid transport, protein targeting, RNA localization (32), nucleobase nucleoside nucleotide and nucleic acid metabolism, intracellular transport (48)
  BMH2 BMH1 + + Energy derivation by oxidation of organic compounds, polysaccharide metabolism, carbohydrate metabolism (6)
  BOI1 BOI2 + + Nuclear organization and biogenesis (22), nucleobase nucleoside nucleotide and nucleic acid transport, protein targeting, RNA localization (32), nucleobase nucleoside nucleotide and nucleic acid metabolism, intracellular transport (48)
  ECI1 DCI1 + + Cytoplasm organization and biogenesis, protein targeting (7)
  GIC2 GIC1 + + Bud growth (6), intracellular signaling cascade (26), signal transduction (58), cytoplasm organization and biogenesis (94)
  GZF3 DAL80 + + Transcription, nitrogen utilization (5), nucleobase nucleoside nucleotide and nucleic acid metabolism (66)
  KCC4 GIN4 + + Cell cycle(16), nucleobase nucleoside nucleotide and nucleic acid metabolism, intracellular transport (48)
  MKK1 MKK2 + + Phosphate metabolism, protein modification (6), conjugation with cellular fusion, sensory perception, perception of abiotic stimulus (20), signal transduction (58), cytoplasm organization and biogenesis (94)
  MYO3 MYO5 + + Polar budding, vesicle-mediated transport, response to osmotic stress (5), cytoplasm organization and biogenesis (10), nucleobase nucleoside nucleotide and nucleic acid metabolism (55)
  NUP100 NUP116 + + Nuclear organization and biogenesis (22), nucleobase nucleoside nucleotide and nucleic acid transport, protein targeting, RNA localization(32), nucleobase nucleoside nucleotide and nucleic acid metabolism, intracellular transport (48)
  PCL6 PCL7 + + Energy derivation by oxidation of organic compounds, polysaccharide metabolism, carbohydrate metabolism (5), transcription (17)
  RAS2 RAS1 + + Intracellular signaling cascade(4), cell proliferation (20)
  RFC3 RFC4 + + DNA repair, response to DNA damage stimulus, cell cycle(18), nucleobase nucleoside nucleotide and nucleic acid metabolism (23)
  SEC4 YPT7 + + Vesicle-mediated transport, secretory pathway, intracellular transport (50)
  SIZ1 NFI1 + + External encapsulating structure organization and biogenesis, cell proliferation, cellular morphogenesis (8), signal transduction (58), cytoplasm organization and biogenesis (94)
  SSK22 SSK2 + + Phosphate metabolism, intracellular signaling cascade, protein modification (5), cell surface receptor linked signal transduction nucleobase nucleoside, nucleotide and nucleic acid metabolism (7)
  SSO2 SSO1 + + Vesicle-mediated transport (14)
  TIF4632 TIF4631 + + Protein biosynthesis (7), macromolecule biosynthesis (12), nucleobase nucleoside nucleotide and nucleic acid metabolism (55)
  VPS64 YLR238W + + Response to pheromone during conjugation with cellular fusion, sensory perception, perception of abiotic stimulus (6), cell cycle, cytoplasm organization and biogenesis (16)
  YIL105C YNL047C + + Unknown (4)
  YPT31 YPT32 + + Vesicle-mediated transport, secretory pathway, intracellular transport (50)
  YPT53 VPS21 + + Cytoplasm organization and biogenesis (6), vesicle-mediated transport, secretory pathway, intracellular transport (50)
  ZDS2 ZDS1 + + Cell aging, response to DNA damage stimulus, chromatin silencing(5), intracellular signaling cascade (26), cytoplasm organization and biogenesis (94), signal transduction (58)
  RPS26B RPS26A + + Nucleobase, nucleoside, nucleotide and nucleic acid metabolism (29)
  YCK1 YCK2 + + Transport (6), nucleobase, nucleoside, nucleotide and nucleic acid metabolism (202)
II BUB1 MAD3 - + Cell cycle, cell proliferation (40), nucleobase, nucleoside, nucleotide and nucleic acid metabolism (66)
  TUB4 TUB1 - + Cell cycle, cytoplasm organization and biogenesis (16)
      Cell cycle, cytoplasm organization and biogenesis (7)
  ENT1 ENT2 - + Cytokinesis, vesicle-mediated transport, cytoplasm organization and biogenesis (4), cell proliferation (20)
      Vesicle-mediated transport (14)
III YAP1802 YAP1801 - - Cell proliferation (20)
      Vesicle-mediated transport (14)
  YMR181C YPL229W - - Cell proliferation (20)
      Transcription (8), nucleobase, nucleoside, nucleotide and nucleic acid metabolism (202)
  NUP170 NUP157 - - Nuclear organization and biogenesis (22), nucleobase nucleoside nucleotide and nucleic acid transport, protein targeting, RNA localization (32), nucleobase nucleoside nucleotide and nucleic acid metabolism, intracellular transport (48)
      Cell cycle, cytoplasm organization and biogenesis (7)
  APP2 GYP5 - - Vesicle-mediated transport (18), transport (21), cytoplasm organization and biogenesis (94)
      RNA metabolism (29), nucleobase, nucleoside, nucleotide and nucleic acid metabolism (202)
  SIR2 HST1 - - Cell cycle, chromatin silencing(6), nucleobase, nucleoside, nucleotide and nucleic acid metabolism (14)
      RNA metabolism (9), nucleobase, nucleoside, nucleotide and nucleic acid metabolism (202)
  GSP1 GSP2 - - Nuclear organization and biogenesis (22), nucleobase, nucleoside, nucleotide and nucleic acid transport, protein targeting, RNA localization(32), nucleobase, nucleoside, nucleotide and nucleic acid metabolism, intracellular transport (48)
      Cell cycle (4)
  SWI5 ACE2 - - Transcription (6), macromolecule biosynthesis (11), nucleobase, nucleoside, nucleotide and nucleic acid metabolism (55)
      Cell cycle (4)
  LSB1 PIN3 - - Unknown (5), nucleobase, nucleoside, nucleotide and nucleic acid metabolism (23)
      RNA metabolism (29), nucleobase, nucleoside, nucleotide and nucleic acid metabolism (202)
  YBR270C BIT61 - - Unknown (4)
      Transport (21), cytoplasm organization and biogenesis (94)
NC EBS1 EST1    
  MTH1 STD1    
  NMA2 NMA1    
  1. + and - indicate the status of the duplicates in respect of their localization in the same PRODISTIN class and whether they have the same cellular functions. NC, not classified, indicating the pairs for which at least one of the genes does not belong to a PRODISTIN class. The last column shows the annotation of the PRODISTIN classes containing the duplicated genes and the number of class members (in parentheses). When the 2 genes of the pair belong to different classes (behavior II and III), the first list of annotations corresponds to the class containing gene 1 and the second list to the one containing gene 2.