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

BMC Bioinformatics

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.

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

ISSN: 1471-2105