Table 3

Statistics for Top, Middle and Bottom Five Scoring Optimized MCODE Predicted Complexes Found in All Known Yeast Protein Interaction Data Set

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

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.

Bader and Hogue BMC Bioinformatics 2003 4:2   doi:10.1186/1471-2105-4-2