Table 3 Statistics for Top, Middle and Bottom Five Scoring Optimized MCODE Predicted Complexes Found in All Known Yeast Protein Interaction Data Set
From: An automated method for finding molecular complexes in large protein interaction networks
Complex Rank | Score | Proteins | Interactions | Density | Cell Role | Cell Localization |
|---|---|---|---|---|---|---|
1 | 10.04 | 46 | 236 | 0.22 | RNA processing/modification and protein degradation (26S Proteasome) | Nuclear |
Protein names | Dbf2,Ecm29,Gcn4,Hsm3,Hyp2,Lhs1,Mkt1,Nas6,Pre1,Pre2,Pre4,Pre5,Pre6, Pre7,Pre8,Pre9,Pup3,Rad23,Rad24,Rad50,Rfc3,Rfc4,Rpn1,Rpn10,Rpn11, Rpn12,Rpn13,Rpn3,Rpn4,Rpn5,Rpn6,Rpn7,Rpn8,Rpn9,Rpt1,Rpt2,Rpt3,Rpt4, Rpt5,Rpt6,Scl1,Ubp6,Ura7,Ygl004c,Yku70,Ypl070w | |||||
2 | 9 | 19 | 90 | 0.51 | RNA processing/modification | Nuclear |
Protein names | Cft1,Cft2,Fip1,Fir1,Hca4,Mpe1,Pap1,Pcf11,Pfs2,Pta1,Pti1,Ref2,Rna14,Ssu72, Uba2,Ufd1,Yor179c,Ysh1,Yth1 | |||||
3 | 7.72 | 56 | 220 | 0.14 | Pol II transcription | Nuclear |
Protein names | Ada2,Adr1,Ahc1,Cdc23,Cdc36,Epl1,Esa1,Fet4,Fun19,Gal4,Gcn5,Hac1,Hfi1, Hhf2,Hht1,Hht2,Ire1,Luc7,Med7,Myo4,Ngg1,Pcf11,Pdr1,Prp40,Rna14,Rpb2, Rpo21,Sap185,Sgf29,Sgf73,Spt15,Spt20,Spt3,Spt7,Spt8,Srb6,Swi5,Taf1,Taf10, Taf11,Taf12,Taf13,Taf14,Taf2,Taf3,Taf5,Taf6,Taf7,Taf8,Taf9,Tra1,Ubp8, Yap1,Yap6,Ybr270c,Yng2 | |||||
4 | 7.58 | 18 | 72 | 0.44 | Cell cycle control, protein degradation, mitosis (Anaphase Promoting Complex) | Nuclear |
Protein names | Apc1,Apc11,Apc2,Apc4,Apc5,Apc9,Cdc16,Cdc23,Cdc26,Cdc27,Dmc1,Doc1, Leu3,Rpt1,Sic1,Spc29,Spt2,Ybr270c | |||||
5 | 7 | 15 | 56 | 0.52 | Vesicular transport (TRAPP Complex) | Golgi |
Protein names | Bet1,Bet3,Bet5,Fks1,Gsg1,Gyp6,Kre11,Sec22,Trs120,Trs130,Trs20,Trs23, Trs31,Trs33,Uso1 | |||||
102 | 3 | 3 | 3 | 1 | RNA splicing | Nuclear |
Protein names | Msl5,Mud2,Smy2 | |||||
103 | 3 | 3 | 3 | 1 | Signal transduction, Cell cycle control, DNA repair, DNA synthesis | Nuclear |
Protein names | Ptc2,Rad53,Ydr071c | |||||
104 | 3 | 3 | 3 | 1 | Cell cycle control, mating response | Uknown |
Protein names | Far3,Vps64,Ynl127w | |||||
105 | 3 | 3 | 3 | 1 | Chromatin/chromosome structure | Nuclear |
Protein names | Gbp2,Hpr1,Mft1 | |||||
106 | 3 | 3 | 3 | 1 | Pol II transcription | Nuclear |
Protein names | Ctk1,Ctk2,Ctk3 | |||||
205 | 2 | 3 | 4 | 1 | Vesicular transport | ER |
Protein names | Rim20,Snf7,Vps4 | |||||
206 | 2 | 3 | 4 | 1 | Protein translocation | Cytoplasmic |
Protein names | Srp14,Srp21,Srp54 | |||||
207 | 2 | 3 | 4 | 1 | Protein translocation | Cytoplasmic |
Protein names | Srp54,Srp68,Srp72 | |||||
208 | 2 | 3 | 4 | 1 | Energy generation | Mitochondrial |
Protein names | Atp1,Atp11,Atp2 | |||||
209 | 2 | 4 | 5 | 0.67 | Nuclear-cytoplasmic and vesicular transport | Varied |
Protein names | Kap123,Nup145,Sec7,Slc1 | |||||