True positives Profile Error rate = FP/(FP + TP) ORF pair MIPS complex ID Complex name Complex size 001101 0.42 YIL033C:YKL166C 110 cAMP-dependent protein kinase 4 010101 0.54 YIL033C:YPL203W 110 cAMP-dependent protein kinase 4 001101 0.42 YOR039W:YOR061W 120_20 Casein kinase II 4 000111 0.57 YBR198C:YGL112C 230_20_20 SAGA complex 14 001111 0.40 YGL112C:YMR236W 230_20_20 SAGA complex 14 110101 0.25 YNL037C:YOR136W 250 Isocitrate dehydrogenase 2 001101 0.42 YKL135C:YPL259C 260_20_10 AP-1 complex 4 000111 0.57 YDL195W:YLR208W 260_30_20 COPII 8 000111 0.57 YBR254C:YKR068C 260_60 TRAPP (Transport Protein Particle) complex 10 001111 0.40 YGL172W:YGR119C 310_10 NSP1 complex 4 010101 0.54 YGR240C:YMR205C 340 Phosphofructokinase 2 000111 0.57 YER094C:YOR157C 360_10 26S proteasome 36 001101 0.42 YDR394W:YGR232W 360_10 26S proteasome 36 001101 0.42 YDR394W:YOR117W 360_10 26S proteasome 36 010101 0.54 YER021W:YPR108W 360_10 26S proteasome 36 100101 0.50 YOR117W:YOR259C 360_10 26S proteasome 36 101011 0.00 YDR394W:YOR259C 360_10 26S proteasome 36 000111 0.57 YCR052W:YFR037C 400 RSC complex (Remodel the structure of chromatin) 10 000111 0.57 YFR037C:YLR321C 400 RSC complex (Remodel the structure of chromatin) 10 010111 0.50 YAR007C:YJL173C 410_40_20 Replication factor A complex 3 000111 0.57 YBR087W:YJR068W 410_40_30 Replication factor C complex 5 001111 0.40 YDR228C:YOR250C 440_10_10 pre mRNA3'-end processing factor CFI 5 011011 0.00 YDR228C:YMR061W 440_10_10 pre mRNA3'-end processing factor CFI 5 001101 0.42 YGL115W:YGL208W 470_10 SNF1 complex 6 001101 0.42 YJR086W:YOR212W 470_30_10 Pheromone response pathway 3 010101 0.54 YHR005C:YOR212W 470_30_10 Pheromone response pathway 3 000111 0.57 YDR211W:YOR260W 500_10_30 eIF2B 5 000111 0.57 YGR083C:YLR291C 500_10_30 eIF2B 5 010101 0.54 YKR026C:YLR291C 500_10_30 eIF2B 5 000111 0.57 YDR429C:YMR146C 500_10_40 eIF3 7 010101 0.54 YDR382W:YLR340W 500_40_10 cytoplasmic ribosomal large subunit 81 110101 0.25 YDL130W:YDR382W 500_40_10 cytoplasmic ribosomal large subunit 81 110101 0.25 YDL130W:YLR340W 500_40_10 cytoplasmic ribosomal large subunit 81 111101 0.00 YDL081C:YLR340W 500_40_10 cytoplasmic ribosomal large subunit 81 001101 0.42 YBL021C:YGL237C 510_160 CCAAT-binding factor complex 4 001101 0.42 YBL021C:YOR358W 510_160 CCAAT-binding factor complex 4 001101 0.42 YGL237C:YOR358W 510_160 CCAAT-binding factor complex 4 001101 0.42 YDR076W:YER095W 510_180_20 other DNA repair complexes 5 000111 0.57 YBR198C:YGL112C 510_190_10_20_10 SAGA complex 14 001111 0.40 YGL112C:YMR236W 510_190_10_20_10 SAGA complex 14 011011 0.00 YBL014C:YJL025W 510_20 Core Factor (CF) 4 000111 0.57 YBR193C:YER022W 510_40_20 Kornberg's mediator (SRB) complex 21 000111 0.57 YER022W:YHR058C 510_40_20 Kornberg's mediator (SRB) complex 21 000111 0.57 YBR198C:YGL112C 510_70_20 TAFIIs 12 000111 0.57 YDR167W:YML098W 510_70_20 TAFIIs 12 001111 0.40 YGL112C:YMR236W 510_70_20 TAFIIs 12 False positives Profile Error rate = FP/(FP + TP) ORF pair 110101 0.25 YGR118W:YKL180W 001111 0.40 YDL043C:YJL203W 001111 0.40 YGL061C:YGR113W 001101 0.42 YBR195C:YPR018W 001101 0.42 YBR217W:YPL149W 001101 0.42 YDR480W:YPL049C 001101 0.42 YHR060W:YLR447C 001101 0.42 YJL110C:YNL021W 001101 0.42 YJR094C:YMR139W 001101 0.42 YLR275W:YPR182W 001101 0.42 YOR159C:YPR182W 010111 0.50 YDL153C:YJR002W 100101 0.50 YML102W:YPR018W 010101 0.54 YBR146W:YIL070C 010101 0.54 YDL116W:YKR082W 010101 0.54 YDL153C:YFL001W 010101 0.54 YDL154W:YFL003C 010101 0.54 YJL166W:YLR295C 010101 0.54 YKL068W:YMR047C 010101 0.54 YLR447C:YPL050C 000111 0.57 YBL020W:YPR086W 000111 0.57 YBR193C:YPR086W 000111 0.57 YDL153C:YGL120C 000111 0.57 YDL153C:YNL216W 000111 0.57 YDR172W:YDR300C 000111 0.57 YDR473C:YPR178W 000111 0.57 YER022W:YFR037C 000111 0.57 YER022W:YLR175W 000111 0.57 YER022W:YMR043W 000111 0.57 YER022W:YNL282W 000111 0.57 YER023W:YLR347C 000111 0.57 YGL122C:YHR089C 000111 0.57 YGR005C:YPR086W 000111 0.57 YGR013W:YKL012W 000111 0.57 YGR099W:YPR086W 000111 0.57 YGR119C:YOL069W 000111 0.57 YHR058C:YPR086W