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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
  1. Score is defined as the product of the complex subgraph density and the number of vertices (proteins) in the complex subgraph (DC × |V|). This ranks larger more dense complexes higher in the results. Density is calculated using the "loop" formula if homodimers exist in the complex, otherwise the "no loop" formula is used. The cell role column is a manual combination of annotation terms for the proteins reported in the complex.