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Table 5 Top predictions not annotated as CCPs in the reference set. The 50 top-scoring protein pairs not annotated in our reference set (so-called "false positives") with results of a further search for pre-existing evidence of CCP. 15 of them are shown to be true CCPs according to YPD.

From: Predicting co-complexed protein pairs using genomic and proteomic data integration

Rank Protein 1 Protein 2 Score YPD Complex Annotation
1 Rpl40Bp Rps31p 0.943  
2 Rps31p Rpl40Ap 0.938  
3 Smc1p Smc3p 0.864 Cohesin
4 Gpt2p Sec28p 0.857  
5 Pwp2p Utp13p 0.844 Small subunit processome
5 Sgn1p Pub1p 0.844  
7 Rdh54p Rad5p 0.833  
7 Arp3p Rvs167p 0.833  
7 Arp3p Srv2p 0.833  
10 Spt5p Rpb3p 0.800 Paf1p complex
10 Spt5p Rpo21p 0.800 Paf1p complex
12 Pwp2p Dip2p 0.776 Small subunit processome
12 Pwp2p Ylr409C 0.776  
12 Sap190p Sap155p 0.776  
12 Sap190p Sap185p 0.776  
12 Pph21p Pph22p 0.776  
12 Nop7p Fpr4p 0.776  
12 Sap185p Sap155p 0.776  
12 Sik1p Cbf5p 0.776  
12 Nop2p Ebp2p 0.776 Pre-60S ribosomal particle
12 Rpa135p Ret1p 0.776  
22 Pwp2p Asc1p 0.750  
22 Drs1p Spb4p 0.750  
24 Rsm10p Mrps5p 0.744 Mrp4p-associated complex (mitochondrial ribosome)
24 Mtr3p Rrp45p 0.744 Exosome 3'-5' exoribonuclease complex
24 Rrp40p Rrp46p 0.744 Exosome 3'-5' exoribonuclease complex
24 Rrp40p Ski6p 0.744 Exosome 3'-5' exoribonuclease complex
28 Fun12p Cbf5p 0.743  
28 Mrpl16p Yml025Cp 0.743  
28 Mrpl1p Mrpl9p 0.743  
28 Mrpl9p Ypl183C-Ap 0.743  
28 Rrp40p Rrp45p 0.743 Exosome 3'-5' exoribonuclease complex
33 Gin4p Kcc4p 0.727  
33 Ecm16p Prp43p 0.727  
35 Rps27Ap Rpl42Bp 0.714  
35 Rps17Bp Rpl36Ap 0.714  
35 Rps4Ap Rpp2Ap 0.714  
35 Dur1,2p Pdb1p 0.714  
35 Rsm7p Mrps5p 0.714 Mrp4p-associated complex (mitochondrial ribosome)
40 Pat1p Lsm2p 0.692 mRNA decay complex
40 Hrp1p Nab2p 0.692  
42 Mrpl1p Mrpl10p 0.684  
42 Mrpl9p Yml025Cp 0.684  
44 Lsm2p Dhh1p 0.667 45S penta-snRNP
44 Pat1p Dhh1p 0.667 45S penta-snRNP
46 Dyn1p Cdc55p 0.667  
46 Emp24p Fks1p 0.667  
46 Yef3p Act1p 0.667  
46 Yef3p Pph22p 0.667  
46 Asc1p Tfp1p 0.667