| node1 | node2 | node1 accession | node2 accession | node1 annotation | node2 annotation | score |
| PRE1 | PRE4 | YER012W | YFR050C | Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle; Belongs to the peptidase T1B family. | Beta 7 subunit of the 20S proteasome; Belongs to the peptidase T1B family. | 0.999 |
| PRE1 | PRE7 | YER012W | YBL041W | Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle; Belongs to the peptidase T1B family. | Beta 6 subunit of the 20S proteasome. | 0.999 |
| PRE1 | PRE9 | YER012W | YGR135W | Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle; Belongs to the peptidase T1B family. | Alpha 3 subunit of the 20S proteasome; the only nonessential 20S subunit; may be replaced by the alpha 4 subunit (Pre6p) under stress conditions to create a more active proteasomal isoform; Belongs to the peptidase T1A family. | 0.999 |
| PRE1 | PUP2 | YER012W | YGR253C | Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle; Belongs to the peptidase T1B family. | Alpha 5 subunit of the 20S proteasome; involved in ubiquitin-dependent catabolism; human homolog is subunit zeta; Belongs to the peptidase T1A family. | 0.999 |
| PRE1 | PUP3 | YER012W | YER094C | Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle; Belongs to the peptidase T1B family. | Beta 3 subunit of the 20S proteasome; involved in ubiquitin-dependent catabolism; human homolog is subunit C10. | 0.999 |
| PRE1 | RPN11 | YER012W | YFR004W | Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle; Belongs to the peptidase T1B family. | Ubiquitin carboxyl-terminal hydrolase RPN11; Metalloprotease subunit of 19S regulatory particle; part of 26S proteasome lid; couples the deubiquitination and degradation of proteasome substrates; involved, independent of catalytic activity, in fission of mitochondria and peroxisomes; protein abundance increases in response to DNA replication stress. | 0.999 |
| PRE1 | RPN12 | YER012W | YFR052W | Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle; Belongs to the peptidase T1B family. | Subunit of the 19S regulatory particle of the 26S proteasome lid; synthetically lethal with RPT1, which is an ATPase component of the 19S regulatory particle; physically interacts with Nob1p and Rpn3p; protein abundance increases in response to DNA replication stress. | 0.999 |
| PRE1 | RPN5 | YER012W | YDL147W | Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle; Belongs to the peptidase T1B family. | Subunit of the CSN and 26S proteasome lid complexes; similar to mammalian p55 subunit and to another S. cerevisiae regulatory subunit, Rpn7p; Rpn5p is an essential protein; the COP9 signalosome is also known as the CSN. | 0.999 |
| PRE1 | SCL1 | YER012W | YGL011C | Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle; Belongs to the peptidase T1B family. | Alpha 1 subunit of the 20S proteasome; involved in the degradation of ubiquitinated substrates; 20S proteasome is the core complex of the 26S proteasome; essential for growth; detected in the mitochondria; Belongs to the peptidase T1A family. | 0.999 |
| PRE1 | UMP1 | YER012W | YBR173C | Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle; Belongs to the peptidase T1B family. | Chaperone required for correct maturation of the 20S proteasome; short-lived chaperone; may inhibit premature dimerization of proteasome half-mers; degraded by proteasome upon completion of its assembly. | 0.999 |
| PRE4 | PRE1 | YFR050C | YER012W | Beta 7 subunit of the 20S proteasome; Belongs to the peptidase T1B family. | Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle; Belongs to the peptidase T1B family. | 0.999 |
| PRE4 | PRE7 | YFR050C | YBL041W | Beta 7 subunit of the 20S proteasome; Belongs to the peptidase T1B family. | Beta 6 subunit of the 20S proteasome. | 0.999 |
| PRE4 | PRE9 | YFR050C | YGR135W | Beta 7 subunit of the 20S proteasome; Belongs to the peptidase T1B family. | Alpha 3 subunit of the 20S proteasome; the only nonessential 20S subunit; may be replaced by the alpha 4 subunit (Pre6p) under stress conditions to create a more active proteasomal isoform; Belongs to the peptidase T1A family. | 0.999 |
| PRE4 | PUP2 | YFR050C | YGR253C | Beta 7 subunit of the 20S proteasome; Belongs to the peptidase T1B family. | Alpha 5 subunit of the 20S proteasome; involved in ubiquitin-dependent catabolism; human homolog is subunit zeta; Belongs to the peptidase T1A family. | 0.999 |
| PRE4 | PUP3 | YFR050C | YER094C | Beta 7 subunit of the 20S proteasome; Belongs to the peptidase T1B family. | Beta 3 subunit of the 20S proteasome; involved in ubiquitin-dependent catabolism; human homolog is subunit C10. | 0.999 |
| PRE4 | RPN11 | YFR050C | YFR004W | Beta 7 subunit of the 20S proteasome; Belongs to the peptidase T1B family. | Ubiquitin carboxyl-terminal hydrolase RPN11; Metalloprotease subunit of 19S regulatory particle; part of 26S proteasome lid; couples the deubiquitination and degradation of proteasome substrates; involved, independent of catalytic activity, in fission of mitochondria and peroxisomes; protein abundance increases in response to DNA replication stress. | 0.999 |
| PRE4 | RPN12 | YFR050C | YFR052W | Beta 7 subunit of the 20S proteasome; Belongs to the peptidase T1B family. | Subunit of the 19S regulatory particle of the 26S proteasome lid; synthetically lethal with RPT1, which is an ATPase component of the 19S regulatory particle; physically interacts with Nob1p and Rpn3p; protein abundance increases in response to DNA replication stress. | 0.999 |
| PRE4 | RPN5 | YFR050C | YDL147W | Beta 7 subunit of the 20S proteasome; Belongs to the peptidase T1B family. | Subunit of the CSN and 26S proteasome lid complexes; similar to mammalian p55 subunit and to another S. cerevisiae regulatory subunit, Rpn7p; Rpn5p is an essential protein; the COP9 signalosome is also known as the CSN. | 0.999 |
| PRE4 | SCL1 | YFR050C | YGL011C | Beta 7 subunit of the 20S proteasome; Belongs to the peptidase T1B family. | Alpha 1 subunit of the 20S proteasome; involved in the degradation of ubiquitinated substrates; 20S proteasome is the core complex of the 26S proteasome; essential for growth; detected in the mitochondria; Belongs to the peptidase T1A family. | 0.999 |
| PRE4 | UMP1 | YFR050C | YBR173C | Beta 7 subunit of the 20S proteasome; Belongs to the peptidase T1B family. | Chaperone required for correct maturation of the 20S proteasome; short-lived chaperone; may inhibit premature dimerization of proteasome half-mers; degraded by proteasome upon completion of its assembly. | 0.999 |