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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.