# Complex name	Complex members (systematic name)	Complex members (standard gene name)	known in GO	known in lit.	comments	pubmed
Spp381-Prp38 complex	YBR152W; YGR075C	SPP381; PRP38	NO	YES	genetic interaction + two-hybrid interaction	9858581
Asf1-Rad53 complex	YJL115W; YPL153C	ASF1; RAD53	NO	YES		11331602; 11172707
Pan1-End3 complex	YIR006C; YNL084C	PAN1; END3	NO	YES		9234686
Sod1-Css1 heterodimer	YJR104C; YMR038C	SOD1; CCS1	NO	YES		11101286
HAT-A4 complex	YBR010W; YBR009C; YNL030W; YEL056W; YPL001W; YLL022C; YOL054W; YNL031C	HHT1; HHF1; HHF2; HAT2; HAT1; HIF1; PSH1; HHT2	NO	YES		9575221
Ste11-Ste50 complex	YLR362W; YCL032W	STE11; STE50	NO	YES		9742096; 9738877
Cdc48-Ufd1-Npl4 complex	YDL126C; YBR170C; YGR048W	CDC48; NPL4; UFD1	NO	YES		11847109
Cdc48-Shp1 complex	YBL058W; YDL126C	SHP1; CDC48	NO	YES		11847109
Sit4-Sap155 complex	YDL047W; YFR040W	SIT4; SAP155	NO	YES		8649382
Ste12-Dig1-Dig2 complex	YPL049C; YHR084W; YDR480W	DIG1; STE12; DIG2	NO	YES		9094309
Rvs161-Rvs167 complex	YCR009C; YDR388W	RVS161; RVS167	NO	YES		9434108; 11096097
She2-She3-Myo4 complex	YAL029C; YBR130C; YKL130C	MYO4; SHE3; SHE2	NO	YES		10792032; 11101531 
Ubp3-Bre5 complex	YNR051C; YER151C	BRE5; UBP3	NO	YES		12778054
Rad6-Rad18 complex	YGL058W; YCR066W	RAD6; RAD18	NO	YES	in GO only part of large proteasome complex, but literature states that RAD18 and RAD6 form a heterodimer that can associate with the proteasome	9287349
Rtt109-Vps75 complex	YLL002W; YNL246W	RTT109; VPS75	NO	YES		18036332
Csm3-Tof1 complex	YMR048W; YNL273W	CSM3; TOF1	NO	YES		14742714
Psr2-Psr1-Whi2 complex	YLR019W; YLL010C; YOR043W	PSR2; PSR1; WHI2	NO	YES	Psr2 is functionally redundant with Psr1p	12090248
Rad23-Png1 complex	YEL037C; YPL096W	RAD23; PNG1	NO	YES		15351714
Tim44-Ssc1 heterodimer	YIL022W; YJR045C	TIM44; SSC1	NO	YES		12677068
Dop1-Mon2 complex	YDR141C; YNL297C	DOP1; MON2	NO	YES		16301316
Rsp5-Ubp2-Rup1 deubiquitinating enzyme complex	YER125W; YOR124C; YOR138C	RSP5; UBP2; RUP1	NO	YES		15933713
Pho80-Pho81-Pho85 CDK-cyclin complex	YGR233C; YOL001W; YPL031C	PHO81; PHO80; PHO85	NO	YES		7939631; 17412959
Trm112-Trm11 complex	YNR046W; YOL124C	TRM112; TRM11	NO	YES		18657261
Dug2-Dug3 complex	YBR281C; YNL191W	DUG2; DUG3	NO	YES		17179087
Dph1-Dph2-Dph3 complex	YBL071W-A; YIL103W; YKL191W	KTI11; DPH1; DPH2	NO	YES	Dph3 is not entirely clear whether it is part of the same complex	15485916
Scs2-Opi1 complex	YER120W; YHL020C	SCS2; OPI1	NO	YES		15455074; 15192221
Ula1-Uba3 enzyme complex	YPL003W; YPR066W	ULA1; UBA3	NO	YES	Ula1-Uba3 form an E1 enzyme pair to activate Rub1p	9545234
Nam1-Sls1 complex	YDL044C; YLR139C	MTF2; SLS1	NO	YES		12637560
ER SNARE Use1	YDR498C; YLR440C; YNL258C; YKL196C; YLR268W; YGL145W; YOR075W; YGL098W	SEC20; SEC39; DSL1; YKT6; SEC22; TIP20; UFE1; USE1	NO	YES	literature seems a bit confusing as to which complexes are specifically formed, but overall it seems that all members associate with oneanother at a given point (although Ykt6 is the most unsure, only shown that it can functionally replace Sec22)	12853481; 9214619; 15958492; 12221135 
Pba1-Pba2 complex	YKL206C; YLR199C; YBR173C	ADD66; PBA1; UMP1	NO	YES	Ump1 which is loosely associated with Pba1-Pba2 functions as an assembly factor	17431397
Gyl1-Gyp5 complex	YMR192W; YPL249C	GYL1; GYP5	NO	YES		15331637
Rtg1-Rtg3 bHLH-Zip complex	YBL103C; YOL067C	RTG3; RTG1	NO	YES		9032238
Sit4-Sap190 complex	YDL047W; YKR028W	SIT4; SAP190	NO	YES		8649382
Rtt103-Rai1-Rat1 complex	YDR289C; YGL246C; YOR048C	RTT103; RAI1; RAT1	NO	YES		15565157
R2TP complex	YCR060W; YHR034C; YDR190C; YPL235W	TAH1; PIH1; RVB1; RVB2	NO	YES		15766533
adenylyl cyclase complex	YJL005W; YNL138W	CYR1; SRV2	NO	YES		2184942
Ssc1-Mge1 complex	YJR045C; YOR232W	SSC1; MGE1	NO	YES		9048947
Dcs1-Dcs2 heterodimer	YLR270W; YOR173W	DCS1; DCS2	NO	YES		15240832
Kap114-Nap1 histone complex	YBL003C; YGL241W; YBL002W; YOL012C; YKR048C	HTA2; KAP114; HTB2; HTZ1; NAP1	NO	YES		12456659
Grh1-Bug1 complex	YDL099W; YDR517W	BUG1; GRH1	NO	YES		17261844
Mad1-Mad2 complex	YGL086W; YJL030W	MAD1; MAD2	NO	YES		10436016
Ic-CPY complex	YLR178C; YMR297W	TFS1; PRC1	NO	YES		4612529; 9521655
Mlh2-Mlh1 heterodimer	YLR035C; YMR167W	MLH2; MLH1	NO	YES		10570173
Sac3-Thp1 complex	YDR159W; YOL072W	SAC3; THP1	NO	YES		12411502
tRNA methyltransferase complex	YDL201W; YDR165W	TRM8; TRM82	NO	YES		12403464
Tlg1 SNARE complex	YBL050W; YDR468C; YGL095C; YOL018C	SEC17; TLG1; VPS45; TLG2	NO	YES		10397773
ribosome-associated complex	YGR285C; YHR064C; YJL080C	ZUO1; SSZ1; SCP160	NO	YES	Scp160 is not known to be in the complex	11274393
Trm9-Trm112 complex	YML014W; YNR046W	TRM9; TRM112	NO	YES		18657261
prohibitin complex	YGR132C; YGR231C	PHB1; PHB2	NO	YES		15525670
succinyl-CoA ligase	YGR244C; YOR142W	LSC2; LSC1	NO	YES		9874242
Gsp1-Prp20 complex	YGL097W; YLR293C; YOR185C	SRM1; GSP1; GSP2	NO	YES	GSP2 is almost identical to Gsp1p	8455603
Kic1-Sog2 complex	YHR102W; YOR353C	KIC1; SOG2	NO	YES		12972564
Nrd1-Nab3-Sen1 termination complex	YLR430W; YNL251C; YPL190C; YMR239C	SEN1; NRD1; NAB3; RNT1	NO	YES	Rnt1 is not known to be in the complex	18660819
Ssk1-Ssk2 complex	YLR006C; YNR031C	SSK1; SSK2	NO	YES		9482735
Vti1-Pep12 complex	YMR197C; YOR036W	VTI1; PEP12	NO	YES		9199167
Pcl7-Pho85 CDK-cyclin complex	YPL031C; YIL050W	PHO85; PCL7	NO	YES		11069666
Prs1-Prs3 heterodimer	YHL011C; YKL181W	PRS3; PRS1	NO	YES		10212224
Vac14-Fig4 complex	YLR386W; YNL325C	VAC14; FIG4	NO	YES		14528018
Cpr6-Hsc82-Sti1-Hsp82 complex	YLR216C; YMR186W; YOR027W; YPL240C	CPR6; HSC82; STI1; HSP82	NO	YES	not entirely clear whether Cpr6 and Sti1 can bind at the same time to Hsp82p. Hsc82 is 97% identical to Hsp82p	9927435
Bur1-Bur2 CDK-cyclin complex	YPR161C; YLR226W	SGV1; BUR2	NO	YES		10982824
Bub1-Bub3 kinase complex	YGR188C; YOR026W	BUB1; BUB3	NO	YES		7969164
Sis2-Ykl088w-Vhs3 complex	YKR072C; YKL088W; YOR054C	SIS2; CAB3; VHS3	NO	YES		14690591
putative Slu7-Prp18 complex	YDR088C; YGR006W	SLU7; PRP18	NO	YES?	SLU7 seems to recruit PRP18 to the spliceosome	12212850
COMA complex	YBR107C; YBR211C; YDR318W; YJR135C; YGR179C; YDR254W; YPL018W; YLR381W; YDR383C; YLR315W; YPR046W	IML3; AME1; MCM21; MCM22; OKP1; CHL4; CTF19; CTF3; NKP1; NKP2; MCM16	subcomplex not defined in GO	YES	together with MIND and Ndc80 constitutes three independent platforms onto which outer kinetochore protons can assemble	14633972
TEL complex	YDR227W; YDL042C	SIR4; SIR2	subcomplex not defined in GO	YES		11500379
nucleoporin Nup84 subcomplex	YGL100W; YDL116W; YGL092W; YKL057C; YJR042W; YLR208W	SEH1; NUP84; NUP145; NUP120; NUP85; SEC13	subcomplex not defined in GO	YES		8565072
Dcp1-Dcp2 decapping enzyme complex	YBR094W; YEL015W; YOL149W; YNL118C	PBY1; EDC3; DCP1; DCP2	subcomplex not defined in GO	YES	Pby1 is not known to be in the same complex	15225544
Ulp1 nuclear pore complex	YLR347C; YMR308C; YPL020C	KAP95; PSE1; ULP1	subcomplex not defined in GO	YES		12471376
TFIIK complex	YDL108W; YDR460W; YPR025C	KIN28; TFB3; CCL1	subcomplex not defined in GO	YES		8001136
Spt6-Spn1 elongator factor complex	YGR116W; YPR133C	SPT6; SPN1	subcomplex not defined in GO	YES		12242279
cleavage factor I complex	YDR228C; YGL044C; YOR250C; YMR061W	PCF11; RNA15; CLP1; RNA14	subcomplex not defined in GO	YES	missing Hrp1p	11344258
Cln-Cdc28 protein kinase complex	YMR199W; YBR160W; YKR091W; YLR210W; YLR079W; YDL155W; YPL256C; YBR135W	CLN1; CDC28; SRL3; CLB4; SIC1; CLB3; CLN2; CKS1	subcomplex not defined in GO	YES		8402888; 9841670
Isw2-Itc1 complex	YGL133W; YOR304W	ITC1; ISW2	subcomplex not defined in GO	YES		11238944
nucleoporin Nup82 subcomplex	YIL115C; YJL061W; YJL041W; YER107C; YMR047C	NUP159; NUP82; NSP1; GLE2; NUP116	subcomplex not defined in GO	YES	Nup116-Gle2 complex associates with nucleoporin subcomplex consisting of Nup82p, Nsp1 and Nup159p	10801828
Snx4-Snx41 heterodimer	YJL036W; YDR425W	SNX4; SNX41	subcomplex not defined in GO	YES		12554655
Nup60-Nup2 nuclear pore complex	YAR002W; YLR335W; YLR347C	NUP60; NUP2; KAP95	subcomplex not defined in GO	YES	Kap60-Kap95 heterodimer dissociates Nup2 from Nup60p	11535617
Erp1-Erp2-Emp24-Erv25 p24 complex	YAL007C; YAR002C-A; YGL200C; YML012W	ERP2; ERP1; EMP24; ERV25	subcomplex not defined in GO	YES		10359606
nucleoporin Nsp1 subcomplex	YFR002W; YGL172W; YGR119C; YJL041W	NIC96; NUP49; NUP57; NSP1	subcomplex not defined in GO	YES		7688296; 9017593
HDA complex	YDR295C; YNL021W; YPR179C	HDA2; HDA1; HDA3	subcomplex not defined in GO	YES		8663039
core H-ACA snoRNP	YDL208W; YHR072W-A; YHR089C; YLR175W; YNL308C	NHP2; NOP10; GAR1; CBF5; KRI1	subcomplex not defined in GO	YES	Kri1 is not known to be in the complex	9843512
Atg11-Atg17-Atg29-Cis1 complex	YPR049C; YPL166W; YDR022C; YLR423C	ATG11; ATG29; CIS1; ATG17	subcomplex not defined in GO	YES	Atg17 forms a ternary complex with Atg29 and Atg31p(Cis1p), Atg11 can recruit Atg17 and Atg29 to the PAS (pre-autophagosomal structure)	18287526
Clathrin	YGL206C; YGR167W	CHC1; CLC1	subcomplex not defined in GO	YES		9845372
Ctf18 RFC-like complex	YCL016C; YHR191C; YMR078C	DCC1; CTF8; CTF18	subcomplex not defined in GO	YES		11389843
commitment complex 2	YKL074C; YLR116W	MUD2; MSL5	subcomplex not defined in GO	YES		10376880
Sec24-Sfb2-Sec16-Sec23 complex	YIL109C; YNL049C; YPL085W; YPR181C	SEC24; SFB2; SEC16; SEC23	subcomplex not defined in GO	YES	Sec23-Sec24 seem to participate in three different complex formations. Sfb2 is functionally redundant with Sec24p	10753972; 8930902
vacuolar proton-transporting V-type ATPase, V0 domain	YPR149W; YKL119C; YLR447C; YOR270C	NCE102; VPH2; VMA6; VPH1	YES	YES	Nce102 is not known to be in the complex	10224039
Hrd1 ubiquitin ligase ERAD-L complex	YDR057W; YLR207W; YOL013C; YML029W	YOS9; HRD3; HRD1; USA1	YES	YES		16873066
anthranilate synthase complex	YER090W; YKL211C	TRP2; TRP3	YES	YES		3881257
nuclear cohesin complex	YJL074C; YFL008W; YIL026C; YDL003W	SMC3; SMC1; IRR1; MCD1	YES	YES		9990856; 9887095; 10499801
protein kinase CK2 complex	YGL019W; YIL035C; YOR039W; YOR061W	CKB1; CKA1; CKB2; CKA2	YES	YES		9427841
phosphatidylinositol 3-kinase complex II	YBR097W; YLR360W; YPL120W; YLR240W	VPS15; VPS38; VPS30; VPS34	YES	YES		11157979
mitochondrial proton-transporting ATP synthase complex	YBL099W; YBR039W; YDR298C; YKL016C	ATP1; ATP3; ATP5; ATP7	YES	YES		10066811
GINS complex	YDR013W; YJL072C; YDR489W; YOL146W	PSF1; PSF2; SLD5; PSF3	YES	YES		12730134
mitochondtrial large ribosomal subunit	YGR076C; YDR405W; YBR282W; YHR147C; YBL038W; YDR462W; YOR150W; YBR122C; YCR071C; YDR237W; YDR116C; YDR322W; YLR439W; YDR296W; YCR046C; YNL252C; YMR193W; YGR220C; YKL167C; YKR006C; YJL063C; YKR085C; YML025C; YMR024W; YNL005C; YLR312W-A; YPL183W-A; YMR098C; YML009C; YMR225C; YNL177C; YNL284C; YPR100W	MRPL25; MRP20; MRPL27; MRPL6; MRPL16; MRPL28; MRPL23; MRPL36; IMG2; MRPL7; MRPL1; MRPL35; MRPL4; MHR1; IMG1; MRPL17; MRPL24; MRPL9; MRP49; MRPL13; MRPL8; MRPL20; YML6; MRPL3; MRP7; MRPL15; RTC6; ATP25; MRPL39; MRPL44; MRPL22; MRPL10; MRPL51	YES	YES		12392552; 9151978
ribonuclease H2 complex	YDR279W; YNL072W	RNH202; RNH201	YES	YES		14734815
SUMO activating enzyme complex	YDR390C; YPR180W	UBA2; AOS1	YES	YES		9312010
tRNA (m1A) methyltransferase complex	YJL125C; YNL062C	GCD14; GCD10	YES	YES		10779558
polarisome	YER149C; YLL021W	PEA2; SPA2	YES	YES		
TRAMP complex	YDL175C; YJL050W; YOL115W	AIR2; MTR4; PAP2	YES	YES		15828860
transcription factor TFIIA complex	YKL058W; YOR194C	TOA2; TOA1	YES	YES		7862117
CPF complex	YMR061W; YER133W; YDR195W; YGR156W; YAL043C; YNL222W; YDR301W; YKL059C; YJR093C; YPR107C; YLR115W; YLR277C; YKR002W; YNL317W; YKL018W; YOR179C	RNA14; GLC7; REF2; PTI1; PTA1; SSU72; CFT1; MPE1; FIP1; YTH1; CFT2; YSH1; PAP1; PFS2; SWD2; SYC1	YES	YES	Rna14 is not known to be in the complex	10523662; 12819204
serine C-palmitoyltransferase complex	YDR062W; YMR296C	LCB2; LCB1	YES	YES		1556076
Cyc8-Tup1 corepressor complex	YCR084C; YBR112C	TUP1; CYC8	YES	YES		9111019; 8943325
delta DNA polymerase complex	YDL102W; YJR006W; YJR043C	POL3; POL31; POL32	YES	YES		
snRNP U2	YDL043C; YJL203W; YMR240C; YDL030W; YPL213W; YML049C; YMR288W	PRP11; PRP21; CUS1; PRP9; LEA1; RSE1; HSH155	YES	YES		11804584; 16314500
AP-3 adaptor complex	YBR288C; YGR261C; YJL024C; YPL195W	APM3; APL6; APS3; APL5	YES	YES		9335339
Ric1-Rgp1 complex	YDR137W; YLR039C	RGP1; RIC1	YES	YES		10990452
Ndc80 complex	YER018C; YIL144W; YOL069W; YMR117C	SPC25; TID3; NUF2; SPC24	YES	YES		11266451; 11179222
Rpd3L complex	YDR207C; YDL076C; YAL013W; YBR095C; YNL097C; YIL084C; YMR263W; YPL181W; YOL004W; YNL330C; YPL139C; YMR075W	UME6; RXT3; DEP1; RXT2; PHO23; SDS3; SAP30; CTI6; SIN3; RPD3; UME1; RCO1	YES	YES		16286007
methionyl glutamyl tRNA synthetase complex	YGL245W; YGL105W; YGR264C	GUS1; ARC1; MES1	YES	YES		11069915; 9659920
protein phosphatase type 2A complex	YAL016W; YDL188C; YGL190C; YDL134C; YMR273C; YML109W; YOR014W	TPD3; PPH22; CDC55; PPH21; ZDS1; ZDS2; RTS1	YES	YES		
TORC1 complex	YHR186C; YJR066W	KOG1; TOR1	YES	YES		12408816
epsilon DNA polymerase complex	YDR121W; YBR278W; YNL262W; YPR175W	DPB4; DPB3; POL2; DPB2	YES	YES		2406268; 11024162
mitochondrial oxoglutarate dehydrogenase complex	YFR049W; YFL018C; YDR148C; YIL125W	YMR31; LPD1; KGD2; KGD1	YES	YES	Ymr31 is not known to bind	2072900
NatC complex	YPR051W; YCR020C-A; YEL053C	MAK3; MAK31; MAK10	YES	YES		10504710
SWR1 complex	YAL011W; YDR485C; YLR085C; YBR231C; YDR334W; YLR385C; YLR399C; YML041C; YFL039C; YDR190C; YPL235W; YJL081C; YGR002C; YNL107W	SWC3; VPS72; ARP6; SWC5; SWR1; SWC7; BDF1; VPS71; ACT1; RVB1; RVB2; ARP4; SWC4; YAF9	YES	YES		
transcription factor TFIIE complex	YKL028W; YKR062W	TFA1; TFA2	YES	YES		
mRNA capping enzyme complex	YPL228W; YGL130W	CET1; CEG1	YES	YES		9710603
Set3C	YBR103W; YDR155C; YIL112W; YKR029C; YGL194C; YOL068C; YCR033W	SIF2; CPR1; HOS4; SET3; HOS2; HST1; SNT1	YES	YES		11711434
ESCRT II complex	YJR102C; YLR417W; YPL002C	VPS25; VPS36; SNF8	YES	YES		12194858
MutSalpha complex	YOL090W; YDR097C	MSH2; MSH6	YES	YES		8816473
Cdc73-Paf1 complex	YBR279W; YGL244W; YOR123C; YOL145C; YLR418C	PAF1; RTF1; LEO1; CTR9; CDC73	YES	YES		9891041
mitochondrial small ribosomal subunit	YER050C; YNR037C; YBR251W; YGR215W; YBR146W; YPL118W; YMR158W; YDR036C; YGR084C; YDL045W-A; YHR059W; YDR041W; YGL129C; YPL013C; YKL155C; YIL093C; YNL137C; YDR337W; YJR101W; YJR113C; YBL090W; YMR188C; YNL081C; YDR175C; YOR158W; YHL004W; YDR347W; YNR036C; YNL306W; YGR165W; YKL003C	RSM18; RSM19; MRPS5; RSM27; MRPS9; MRP51; MRPS8; EHD3; MRP13; MRP10; FYV4; RSM10; RSM23; MRPS16; RSM22; RSM25; NAM9; MRPS28; RSM26; RSM7; MRP21; MRPS17; SWS2; RSM24; PET123; MRP4; MRP1; MRPS12; MRPS18; MRPS35; MRP17	YES	YES		9151978; 9445368; 11278769
AP-1 adaptor complex	YFL034W; YHL019C; YKL135C; YLR170C; YPR029C; YPL259C	YFL034W; APM2; APL2; APS1; APL4; APM1	YES	YES		10564262
U4-U6 x U5 tri-snRNP complex	YGR074W; YER029C; YLR147C; YLR275W; YER172C; YKL173W; YHR165C; YDL098C; YGR091W; YDR473C; YOR308C; YBR055C; YPR178W; YPR082C	SMD1; SMB1; SMD3; SMD2; BRR2; SNU114; PRP8; SNU23; PRP31; PRP3; SNU66; PRP6; PRP4; DIB1	YES	YES		10377396; 10449419
GET complex	YDL100C; YER083C; YGL020C	GET3; GET2; GET1	YES	YES		16269340
NatB complex	YOL076W; YPR131C	MDM20; NAT3	YES	YES		12890471
heterotrimeric G-protein complex	YHR005C; YOR212W	GPA1; STE4	YES	YES		11394869; 2105453
ribonuclease MRP complex	YBL018C; YAL033W; YBR167C; YBR257W; YGR030C; YNL221C; YNL282W; YDR478W; YHR062C	POP8; POP5; POP7; POP4; POP6; POP1; POP3; SNM1; RPP1	YES	YES		9620854; 15637077; 9353260; 9029160
DASH complex	YDR201W; YDR016C; YKL052C; YGR113W; YGL061C; YKR083C; YKR037C; YKL138C-A; YBR233W-A	SPC19; DAD1; ASK1; DAM1; DUO1; DAD2; SPC34; HSK3; DAD3	YES	YES		11799062; 15640796; 15664196
COPI vesicle coat	YER122C; YGL137W; YDL145C; YDR238C; YNL287W; YFR051C; YIL076W; YPL010W	GLO3; SEC27; COP1; SEC26; SEC21; RET2; SEC28; RET3	YES	YES		15254269; 8617224; 7929113
GID complex	YCL039W; YDL176W; YDR255C; YBR105C; YGL227W; YIL097W; YIL017C; YMR135C	GID7; YDL176W; RMD5; VID24; VID30; FYV10; VID28; GID8	YES	YES	Only recently found in literature (2008), YDL176W not part of this	18508925
alpha-glucosidase II complex	YBR229C; YDR221W	ROT2; GTB1	YES	YES		
Golgi transport complex	YNL041C; YPR105C; YGL005C; YGL223C; YER157W; YNL051W; YGR120C; YML071C	COG6; COG4; COG7; COG1; COG3; COG5; COG2; COG8	YES	YES		11703943
mitochondrial processing peptidase complex	YHR024C; YLR163C	MAS2; MAS1	YES	YES		2905264
carbamoyl-phosphate synthase complex	YJR109C; YOR303W	CPA2; CPA1	YES	YES		6086650; 6358221
mitochondrial pyruvate dehydrogenase complex	YBR221C; YER178W; YNL071W; YGR193C	PDB1; PDA1; LAT1; PDX1	YES	YES		9123965; 2007123
Srb-mediator complex	YBL093C; YDL005C; YGL127C; YCR081W; YGR104C; YDR308C; YER022W; YGL025C; YOL051W; YPR168W; YMR112C; YDR443C; YBR253W; YOL135C; YLR071C; YPL042C; YHR041C; YHR058C; YBR193C; YOR174W; YPR070W; YNR010W; YGL151W; YNL236W	ROX3; MED2; SOH1; SRB8; SRB5; SRB7; SRB4; PGD1; GAL11; NUT2; MED11; SSN2; SRB6; MED7; RGR1; SSN3; SRB2; MED6; MED8; MED4; MED1; CSE2; NUT1; SIN4	YES	YES		9420330; 16885025
CCR4-NOT complex	YGR134W; YCR093W; YAL021C; YNL288W; YNR052C; YER068W	CAF130; CDC39; CCR4; CAF40; POP2; MOT2	YES	YES		10490603
ubiquitin conjugating enzyme complex	YGL087C; YMR140W; YDR092W	MMS2; SIP5; UBC13	YES	YES	Sip5 not known to be part of complex	10089880
MBF transcription complex	YDL056W; YLR182W	MBP1; SWI6	YES	YES		9719633
mitochondrial respiratory chain complex II	YKL148C; YLL041C	SDH1; SDH2	YES	YES		
snf1 protein kinase complex	YDR028C; YDR422C; YER027C; YER129W; YDR477W; YGL115W; YGL208W	REG1; SIP1; GAL83; SAK1; SNF1; SNF4; SIP2	YES	YES	Reg1 and Sak1 are not known to be in the complex. Sak1 is an upstream kinase that can activate Snf1p	12393914
m-AAA complex	YER017C; YMR089C	AFG3; YTA12	YES	YES		8681382
ESCRT-0 complex	YHL002W; YNR006W	HSE1; VPS27	YES	YES		12055639
TREX complex	YDR381W; YDL084W; YDR138W; YHR167W; YML062C; YNL139C; YNL253W; YNL004W	YRA1; SUB2; HPR1; THP2; MFT1; THO2; TEX1; HRB1	YES	YES	Hrb1 is not known to be in the complex	11979277
alpha DNA polymerase:primase complex	YBL035C; YNL102W; YIR008C; YKL045W	POL12; POL1; PRI1; PRI2	YES	YES		3888995
NatA complex	YDL040C; YHR013C; YOR253W	NAT1; ARD1; NAT5	YES	YES		14517307
signal recognition particle	YDL051W; YKL122C; YML105C; YPR088C; YDL092W; YPL210C; YPL243W	LHP1; SRP21; SEC65; SRP54; SRP14; SRP72; SRP68	YES	YES	Lhp1 is not known to be in the complex	
NEF4 complex	YJR052W; YPL046C	RAD7; ELC1	YES	YES	missing Abf1 and Rad16	15226437
CCAAT-binding factor complex	YBL021C; YGL237C; YOR358W	HAP3; HAP2; HAP5	YES	YES		9618445
vacuolar proton-transporting V-type ATPase, V1 domain	YJR033C; YDL185W; YBR127C; YGR020C; YHR039C-A; YEL051W; YPR036W; YOR332W; YKL080W	RAV1; TFP1; VMA2; VMA7; VMA10; VMA8; VMA13; VMA4; VMA5	YES	YES		9442887
PAN complex	YGL094C; YKL025C	PAN2; PAN3	YES	YES		8816488
cytosolic small ribosomal subunit	YDR025W; YER102W; YBR048W; YBR189W; YBL072C; YDR064W; YOR096W; YJR145C; YHR203C; YJL190C; YIL069C; YLR367W; YML024W; YPL081W; YOR204W	RPS11A; RPS8B; RPS11B; RPS9B; RPS8A; RPS13; RPS7A; RPS4A; RPS4B; RPS22A; RPS24B; RPS22B; RPS17A; RPS9A; DED1	YES	YES		9559554; 3533916
gamma-tubulin small complex, spindle pole body	YAL047C; YHR172W; YNL126W; YLR212C	SPC72; SPC97; SPC98; TUB4	YES	YES		9384578
Elg1 RFC-like complex	YBR087W; YOL094C; YNL290W; YJR068W; YOR217W; YOR144C	RFC5; RFC4; RFC3; RFC2; RFC1; ELG1	YES	YES		12912927
tRNA-intron endonuclease complex	YLR105C; YPL083C	SEN2; SEN54	YES	YES		9200603
ISW1 complex	YBR245C; YKR001C; YPL082C; YLR095C; YMR044W	ISW1; VPS1; MOT1; IOC2; IOC4	YES	YES		12482963
EKC-KEOPS protein complex	YGR262C; YJL184W; YKR038C; YML036W	BUD32; GON7; KAE1; CGI121	YES	YES		16874308
FACT complex	YGL207W; YML069W	SPT16; POB3	YES	YES		11432837
HOPS complex	YMR231W; YAL002W; YLR396C; YLR148W; YDR080W; YDL077C; YPL045W	PEP5; VPS8; VPS33; PEP3; VPS41; VAM6; VPS16	YES	YES	shares many subunits with CORVET complex, HOPS and CORVET complex can interconvert	10944212; 17488625
MutSBeta complex	YOL090W; YCR092C	MSH2; MSH3	YES	YES		8805366
cytochome c oxidase complex, subunits IV, Va, VI and VIIa	YNL052W; YGL187C; YDL067C; YHR051W	COX5A; COX4; COX9; COX6	YES	YES	total number of cytochrom c oxidase amounts to 12, but most are easily lost due to purification techniques	1331058
SCF ubiquitin ligase complex	YDL132W; YDR054C; YJL047C; YGL252C; YOL133W	CDC53; CDC34; RTT101; RTG2; HRT1	YES	YES		9346238; 10385629
nucleotide-excision repair factor 1 complex	YAL027W; YML095C; YPL022W	SAW1; RAD10; RAD1	YES	YES		8621533
carboxy-terminal domain protein kinase complex	YKL139W; YJL006C; YML112W	CTK1; CTK2; CTK3	YES	YES		
eukaryotic translation elongation factor 1 complex	YAL003W; YPL048W; YKL081W; YPR080W	EFB1; CAM1; TEF4; TEF1	YES	YES		8420802; 3026912; 8041634 
NuA4 histone acetyltransferase complex	YDR359C; YEL018W; YFL024C; YOR244W; YJR082C; YHR090C; YNL136W; YPR023C; YJL081C; YGR002C; YNL107W; YFL039C	EAF1; EAF5; EPL1; ESA1; EAF6; YNG2; EAF7; EAF3; ARP4; SWC4; YAF9; ACT1	YES	YES		10487762
RNA polymerase I complex	YNL113W; YPR110C; YHR143W-A; YBR154C; YPR187W; YOR224C; YOR210W; YDR156W; YJL148W; YJR063W; YNL248C; YOR340C; YOR341W; YPR010C	RPC19; RPC40; RPC10; RPB5; RPO26; RPB8; RPB10; RPA14; RPA34; RPA12; RPA49; RPA43; RPA190; RPA135	YES	YES		9774381; 8246845
90S preribosome	YBR247C; YDR324C; YPL126W; YOR310C; YGR145W; YLR222C; YNL075W; YJL109C; YDR398W; YCR057C; YPR144C; YLR409C; YNL132W; YLL011W; YDL148C; YOR145C; YBL004W; YLR186W; YCL059C; YJR145C; YDR449C; YPR112C; YMR128W; YJR002W; YDR299W; YOR096W; YPL217C; YLR197W; YOR078W; YDL014W; YPR137W; YMR093W; YOL010W; YPL266W; YLR003C; YJL069C; YGR128C; YLR129W; YGR090W; YPL012W; YER127W; YKR060W; YER082C; YEL055C; YDR064W; YHR196W; YGL171W; YHR148W	ENP1; UTP4; NAN1; NOP58; ENP2; UTP13; IMP4; UTP10; UTP5; PWP2; NOC4; UTP21; KRE33; SOF1; NOP14; PNO1; UTP20; EMG1; KRR1; RPS4A; UTP6; MRD1; ECM16; MPP10; BFR2; RPS7A; BMS1; NOP56; BUD21; NOP1; RRP9; UTP15; RCL1; DIM1; CMS1; UTP18; UTP8; DIP2; UTP22; RRP12; LCP5; UTP30; UTP7; POL5; RPS13; UTP9; ROK1; IMP3	YES	YES		12150911
RSC complex	YMR091C; YGL013C; YNR023W; YHR056C; YLR357W; YML127W; YDR303C; YDR225W; YOR156C; YGR056W; YFR037C; YOR290C; YIL126W; YHL025W; YJL176C; YMR033W; YDR073W; YCR020W-B; YPR034W; YCR052W; YBR289W; YLR321C; YLR033W; YGR275W; YFL049W; YPL016W; YKR008W	NPL6; PDR1; SNF12; RSC30; RSC2; RSC9; RSC3; HTA1; NFI1; RSC1; RSC8; SNF2; STH1; SNF6; SWI3; ARP9; SNF11; HTL1; ARP7; RSC6; SNF5; SFH1; RSC58; RTT102; SWP82; SWI1; RSC4	YES	YES		12183366; 10619019
CAAX-protein geranylgeranyltransferase complex	YKL019W; YGL155W	RAM2; CDC43	YES	YES		1400380
Arp2-3 protein complex	YDL029W; YBR234C; YIL062C; YNR035C; YKL013C; YLR370C; YJR065C	ARP2; ARC40; ARC15; ARC35; ARC19; ARC18; ARP3	YES	YES		
SAGA complex	YBR198C; YDR167W; YDR145W; YMR236W; YDR448W; YGR252W; YGL112C; YDR392W; YCL010C; YOL148C; YBR081C; YDR176W; YGL066W; YPL254W; YLR055C; YMR223W; YPL047W; YHR099W	TAF5; TAF10; TAF12; TAF9; ADA2; GCN5; TAF6; SPT3; SGF29; SPT20; SPT7; NGG1; SGF73; HFI1; SPT8; UBP8; SGF11; TRA1	YES	YES		9674426
TRAPP complex	YGR166W; YKR068C; YOR115C; YDR108W; YDR246W; YML077W; YDR407C; YBR254C; YDR472W; YMR218C	KRE11; BET3; TRS33; GSG1; TRS23; BET5; TRS120; TRS20; TRS31; TRS130	YES	YES		10727015
AP-2 adaptor complex	YBL037W; YJR058C; YJR005W; YOL062C	APL3; APS2; APL1; APM4	YES	YES		10564262
CAF-1 complex	YBR195C; YML102W; YPR018W	MSI1; CAC2; RLF2	YES	YES		9030687
GARP complex	YDR484W; YDR027C; YJL029C; YJL034W; YKR020W	VPS52; VPS54; VPS53; KAR2; VPS51	YES	YES		10637310
CCR4-NOT Not2-Not5 subcomplex	YDL165W; YPR072W	CDC36; NOT5	YES	YES	Not2 and Not5 are known to have a strong physical association	10490603
origin recognition complex	YBR060C; YML065W; YLL004W; YPR162C; YHR118C; YNL261W	ORC2; ORC1; ORC3; ORC4; ORC6; ORC5	YES	YES		
Smc5-Smc6 complex	YEL019C; YDR288W; YOL034W; YDL105W	MMS21; NSE3; SMC5; NSE4	YES	YES		15738391
RNA polymerase III complex	YDR045C; YDL150W; YJL011C; YKL144C; YKR025W; YNL151C; YPR190C; YNR003C; YOR207C; YOR116C; YNL113W; YPR110C; YBR154C; YPR187W; YOR224C; YOR210W	RPC11; RPC53; RPC17; RPC25; RPC37; RPC31; RPC82; RPC34; RET1; RPO31; RPC19; RPC40; RPB5; RPO26; RPB8; RPB10	YES	YES		9774381; 8246845
proteasome regulatory particle	YDL147W; YHL030W; YDR363W-A; YFR010W; YGR232W; YDR394W; YER021W; YDR427W; YDL007W; YHR200W; YFR004W; YFR052W; YOR259C; YOR261C; YDL097C; YGL048C; YLR421C; YHR027C; YOR117W; YPR108W; YIL075C; YKL145W	RPN5; ECM29; SEM1; UBP6; NAS6; RPT3; RPN3; RPN9; RPT2; RPN10; RPN11; RPN12; RPT4; RPN8; RPN6; RPT6; RPN13; RPN1; RPT5; RPN7; RPN2; RPT1	YES	YES		
Ski complex	YGL213C; YLR398C; YKL023W; YPR189W	SKI8; SKI2; YKL023W; SKI3	YES	YES	Ykl023w is not known to be in the complex	
eukaryotic translation initiation factor 2B complex	YDR211W; YLR215C; YOR260W; YLR291C; YGR083C; YJR007W; YER025W; YKR026C; YPL237W	GCD6; CDC123; GCD1; GCD7; GCD2; SUI2; GCD11; GCN3; SUI3	YES	YES	eIF-2B phosphorylates eIF-2 and is stably associated with eIF-2 alpha	8506384; 8336705
exomer complex	YLR330W; YJL099W; YKR027W; YOR299W; YMR237W	CHS5; CHS6; BCH2; BUD7; BCH1	YES	YES		
INO80 complex	YFL039C; YER092W; YGL150C; YDL002C; YFL013C; YOR141C; YLR052W; YNL059C; YNL215W; YDR190C; YPL235W; YJL081C	ACT1; IES5; INO80; NHP10; IES1; ARP8; IES3; ARP5; IES2; RVB1; RVB2; ARP4	YES	YES		10952318
MIND complex	YAL034W-A; YPL233W; YIR010W; YJR112W	MTW1; NSL1; DSN1; NNF1	YES	YES		14633972
Elongator holoenzyme complex	YLR384C; YGR200C; YPL086C; YHR187W; YPL101W; YMR312W	IKI3; ELP2; ELP3; IKI1; ELP4; ELP6	YES	YES		
retromer complex	YHR012W; YJL154C; YJL053W; YOR069W; YOR132W; YPL070W	VPS29; VPS35; PEP8; VPS5; VPS17; MUK1	YES	YES		9700157
anaphase-promoting complex	YDR260C; YFR036W; YIR025W; YGL240W; YBL084C; YDR118W; YOR249C; YHR166C; YKL022C; YLR127C; YNL172W; YLR102C	SWM1; CDC26; MND2; DOC1; CDC27; APC4; APC5; CDC23; CDC16; APC2; APC1; APC9	YES	YES		9469814; 12574115; 15797379
proteasome core complex	YFL007W; YER012W; YGL011C; YBL041W; YOL038W; YFR050C; YGR135W; YER094C; YJL001W; YOR362C; YPR103W; YGR253C; YML092C; YOR157C; YMR314W	BLM10; PRE1; SCL1; PRE7; PRE6; PRE4; PRE9; PUP3; PRE3; PRE10; PRE2; PUP2; PRE8; PUP1; PRE5	YES	YES	Evidence based on computational method	
alpha-1,6-mannosyltransferase complex	YDR245W; YEL036C; YJL183W; YPL050C; YJR075W	MNN10; ANP1; MNN11; MNN9; HOC1	YES	YES		9430634; 10037752
ESCRT I complex	YCL008C; YLR119W; YGR206W; YPL065W	STP22; SRN2; MVB12; VPS28	YES	YES		11511343
cAMP-dependent protein kinase complex	YKL166C; YIL033C; YJL164C; YPL203W	TPK3; BCY1; TPK1; TPK2	YES	YES		3036373
translation release factor complex	YBR143C; YDR172W	SUP45; SUP35	YES	YES		7556078
Ku70:Ku80 complex	YMR106C; YMR284W	YKU80; YKU70	YES	YES		8754818
transcription factor TFIIIC complex	YGR047C; YAL001C; YDR362C; YBR123C; YOR110W; YPL007C	TFC4; TFC3; TFC6; TFC1; TFC7; TFC8	YES	YES		10384303
fatty acid synthase complex	YKL182W; YPL231W	FAS1; FAS2	YES	YES		65153
RENT complex	YDL042C; YJL076W	SIR2; NET1	YES	YES		10219244
septin complex	YJR092W; YJR076C; YCR002C; YHR107C; YDL225W; YLR314C	BUD4; CDC11; CDC10; CDC12; SHS1; CDC3	YES	YES	Bud4 is not known to be part of the complex	9813094; 18550837
exocyst	YPR055W; YER008C; YJL085W; YIL068C; YDR166C; YLR166C; YBR102C; YGL233W	SEC8; SEC3; EXO70; SEC6; SEC5; SEC10; EXO84; SEC15	YES	YES		8978675
signalosome	YDR179C; YDL216C; YOL117W; YIL071C; YMR025W	CSN9; RRI1; RRI2; PCI8; CSI1	YES	YES		12446563
preribosome, large subunit precursor	YLL008W; YER006W; YPL211W; YBR142W; YNL061W; YNL110C; YOL077C; YDR496C; YHR052W; YMR290C; YKR081C; YLL034C; YOR272W; YKL172W; YPR016C; YDR087C; YGL111W; YHR088W; YLR002C; YFL002C; YKL009W; YCL054W; YDL031W; YPL093W; YOR206W; YLR449W; YMR049C; YNL002C; YMR229C; YGR103W	DRS1; NUG1; NIP7; MAK5; NOP2; NOP15; BRX1; PUF6; CIC1; HAS1; RPF2; RIX7; YTM1; EBP2; TIF6; RRP1; NSA1; RPF1; NOC3; SPB4; MRT4; SPB1; DBP10; NOG1; NOC2; FPR4; ERB1; RLP7; RRP5; NOP7	YES	YES		
nucleotide-excision repair factor 2 complex	YEL037C; YER162C	RAD23; RAD4	YES	YES		7768886
calcineurin complex	YKL190W; YML057W	CNB1; CMP2	YES	YES		1321337
mitochondrial isocitrate dehydrogenase complex (NAD+)	YOR136W; YNL037C	IDH2; IDH1	YES	YES		16884682
Mre11 complex	YDR369C; YMR224C	XRS2; MRE11	YES	YES	missing Rad50	9845372
Rab-protein geranylgeranyltransferase complex	YJL031C; YPR176C	BET4; BET2	YES	YES		8756702
signal recognition particle receptor complex	YDR292C; YKL154W	SRP101; SRP102	YES	YES		9679135
endoplasmic reticulum Sec complex	YBR171W; YLR292C; YOR254C; YPL094C	SEC66; SEC72; SEC63; SEC62	YES	YES		2000150; 8257795 ; 8051213
eukaryotic translation initiation factor 3 complex	YAL035W; YDR091C; YBR079C; YMR309C; YLR192C; YDR429C; YMR146C; YPR041W; YOR361C; YNL244C	FUN12; RLI1; RPG1; NIP1; HCR1; TIF35; TIF34; TIF5; PRT1; SUI1	YES	YES	Fun12 and Rli1 are not known to be in the complex but are required for translation initiation	9660829
HIR complex	YBL008W; YOR038C; YBR215W; YJR140C	HIR1; HIR2; HPC2; HIR3	YES	YES		16303565; 16264190
MutLalpha complex	YMR167W; YNL082W	MLH1; PMS1	YES	YES		10570173
RNA polymerase II complex	YGL043W; YDL115C; YDL140C; YGL070C; YGR005C; YGR186W; YIL021W; YDR404C; YOL005C; YJL140W; YOR151C; YGR063C; YML010W; YPL129W; YBR154C; YPR187W; YOR224C; YOR210W	DST1; IWR1; RPO21; RPB9; TFG2; TFG1; RPB3; RPB7; RPB11; RPB4; RPB2; SPT4; SPT5; TAF14; RPB5; RPO26; RPB8; RPB10	YES	YES		9774381; 8246845
chaperonin-containing T-complex	YJL014W; YDL143W; YDR188W; YIL142W; YJL111W; YOR281C; YNL212W; YJL008C; YJR064W	CCT3; CCT4; CCT6; CCT2; CCT7; PLP2; VID27; CCT8; CCT5	YES	YES	Plp1 and Vid27 are not known to be in the complex	15704212
transcription factor TFIID complex	YBR198C; YDR167W; YDR145W; YMR236W; YGL112C; YGR274C; YMR227C; YML015C; YPL011C; YMR005W; YML098W	TAF5; TAF10; TAF12; TAF9; TAF6; TAF1; TAF7; TAF11; TAF3; TAF4; TAF13	YES	YES		15448131; 10788514
nascent polypeptide-associated complex	YHR193C; YPL037C; YDR252W	EGD2; EGD1; BTT1	YES	YES		
cytosolic large ribosomal subunit	YBL092W; YGL014W; YBR191W; YHR141C; YLR287C-A; YFR032C-A; YGR118W; YNL302C; YNL096C; YGL031C; YDR418W; YGL123W; YDR382W; YDL083C; YCR031C; YDR447C; YER074W; YBL027W; YDL136W; YHL001W; YJL177W; YGR034W; YMR194W; YKL180W; YBR181C; YOL040C; YHL033C; YFR031C-A; YNL069C; YML073C; YLR448W; YNL301C; YLR075W; YML063W; YLR441C; YJR123W; YNL178W; YPL090C; YLR150W; YGL147C; YBR031W; YGL030W; YDL075W; YGL103W; YDL082W; YDR471W; YMR242C; YOL127W; YGL135W; YGR085C; YIL133C; YLR029C; YDR012W; YOR312C; YGL076C; YLL045C; YOR063W; YPL198W; YPL249C-A; YLR340W; YIL018W; YPL220W; YMR142C; YOL039W	RPL32; PUF4; RPL21A; RPL42B; RPS30A; RPL29; RPS23A; RPS19B; RPS7B; RPL24A; RPL12B; RPS2; RPP2B; RPS16B; RPS14A; RPS17B; RPS24A; RPL19B; RPL35B; RPL14B; RPL17B; RPL26B; RPL36A; RPL17A; RPS6B; RPS15; RPL8A; RPL2A; RPL16B; RPL6A; RPL6B; RPL18B; RPL10; RPS1B; RPS1A; RPS5; RPS3; RPS6A; STM1; RPL9A; RPL4A; RPL30; RPL31A; RPL28; RPL13A; RPL27B; RPL20A; RPL25; RPL1B; RPL11B; RPL16A; RPL15A; RPL4B; RPL20B; RPL7A; RPL8B; RPL3; RPL7B; RPL36B; RPP0; RPL2B; RPL1A; RPL13B; RPP2A	YES	YES		9559554; 10690410
RAVE complex	YDR202C; YJR033C; YDR328C	RAV2; RAV1; SKP1	YES	YES		11283612
prefoldin complex	YJL179W; YEL003W; YGR078C; YNL153C; YML094W; YLR200W	PFD1; GIM4; PAC10; GIM3; GIM5; YKE2	YES	YES		9463374; 9630229
eukaryotic translation initiation factor 4F complex	YER165W; YGL049C; YGR162W; YOL139C	PAB1; TIF4632; TIF4631; CDC33	YES	YES	Pab1 is known to be associated with TIF4632-1, but not officially annotated as part of the complex. missing Tif1-2p	8336723; 9841679
core TFIIH complex	YDR311W; YLR005W; YPR056W	TFB1; SSL1; TFB4	YES	YES	missing Rad3 and Tfb2p	14500720
phenylalanine-tRNA ligase complex	YLR060W; YFL022C	FRS1; FRS2	YES	YES		9812975
DNA replication factor A complex	YAR007C; YNL312W; YJL173C; YHR164C	RFA1; RFA2; RFA3; DNA2	YES	YES	Dna2 not known to be part of the complex	2554144
alpha,alpha-trehalose-phosphate synthase complex (UDP-forming)	YBR126C; YDR074W; YMR261C; YML100W	TPS1; TPS2; TPS3; TSL1	YES	YES		
GPI-anchor transamidase complex	YDR331W; YHR188C; YLR088W; YDR434W	GPI8; GPI16; GAA1; GPI17	YES	YES		
ribonucleoside-diphosphate reductase complex	YGR180C; YJL026W; YOR230W	RNR4; RNR2; WTM1	YES	YES	Wtm1 is transcriptional modulator of RNR genes	10716984
exosome (RNase complex)	YHR081W; YCR035C; YGR195W; YDL111C; YDR280W; YOR076C; YGR158C; YHR069C; YGR095C; YOL142W; YNL232W; YOL021C; YOR001W; YNR024W; YNL189W	LRP1; RRP43; SKI6; RRP42; RRP45; SKI7; MTR3; RRP4; RRP46; RRP40; CSL4; DIS3; RRP6; MPP6; SRP1	YES	YES		10465791
COMPASS complex	YBR175W; YBR258C; YDR469W; YHR119W; YAR003W; YLR015W; YPL138C; YKL018W	SWD3; SHG1; SDC1; SET1; SWD1; BRE2; SPP1; SWD2	YES	YES		11687631
SBF transcription complex	YER111C; YLR182W	SWI4; SWI6	YES	YES		8423776
protein farnesyltransferase complex	YDL090C; YKL019W	RAM1; RAM2	YES	YES		1763050
nuclear condensin complex	YFR031C; YDR325W; YLR272C; YLR086W; YBL097W	SMC2; YCG1; YCS4; SMC4; BRN1	YES	YES		10811823
snRNP U6	YER146W; YDL160C; YER112W; YCR077C; YJL124C; YBL026W; YDR378C; YNL147W; YJR022W; YMR268C; YLR438C-A	LSM5; DHH1; LSM4; PAT1; LSM1; LSM2; LSM6; LSM7; LSM8; PRP24; LSM3	YES	YES		10369684; 11720284; 10580475
subunit VII of the cytochrome bc1 complex	YDL189W; YDR529C; YBL045C; YPR191W	RBS1; QCR7; COR1; QCR2	YES, not split u in subunits	YES	Rbs1 not known to be in the same complex	10873857
putatie Saf1-Aah1 complex	YNL141W; YBR280C	AAH1; SAF1	NO	NO, double check!	Aah1 is specifically degraded through Saf1 and has been suggested as a bonafide subunit of Skp1-Cullin-F-box	17517885
putative Tkl2-Tkl1 isozyme complex	YBR117C; YPR074C	TKL2; TKL1	NO	NO		
putative Trm7-Ymr259c complex	YBR061C; YMR259C	TRM7; YMR259C	NO	NO		
putative Atg18-Atg2 complex	YFR021W; YNL242W	ATG18; ATG2	NO	NO	Atg2 is recruited by Atg18	
putative Trm7-Rtt10 complex	YBR061C; YPL183C	TRM7; RTT10	NO	NO		
putative Nuc1-Trz1-Ymr099c complex	YJL208C; YKR079C; YMR099C	NUC1; TRZ1; YMR099C	NO	NO		
putative Sas5-Wtm2 complex	YOR213C; YOR229W	SAS5; WTM2	NO	NO		
putative Cdc47-Erg26 complex	YBR202W; YGL001C	MCM7; ERG26	NO	NO		
putative Flc2-Tcb3 complex	YAL053W; YML072C	FLC2; TCB3	NO	NO		
putative Rpl23a-Rpl23b-Bcp1-Rkm1 complex	YBL087C; YER117W; YDR361C; YPL208W	RPL23A; RPL23B; BCP1; RKM1	NO	NO	Rpl23a and Rpl23b are identical. Rkm1 methylates lysine residues of Rpl23a-bp	
putative Rsa3-Urb1-Urb2-Nop8 complex	YLR221C; YKL014C; YJR041C; YOL144W	RSA3; URB1; URB2; NOP8	NO	NO	most proteins involed in pre-60S ribosome biogenesis	
putative Ybr225w-Mds3-Cdc25 complex	YBR225W; YGL197W; YLR310C	YBR225W; MDS3; CDC25	NO	NO		
putative Tom71-Ylr072w complex	YHR117W; YLR072W	TOM71; YLR072W	NO	NO		
putative Flc2-Pdr5 complex	YAL053W; YOR153W	FLC2; PDR5	NO	NO		
putative Ecm30-Ubp15 complex	YLR436C; YMR304W	ECM30; UBP15	NO	NO		
putative Cox20-Chs1 complex	YDR231C; YNL192W	COX20; CHS1	NO	NO		
putative Hca4-Esf1-Esf2 complex	YJL033W; YDR365C; YNR054C	HCA4; ESF1; ESF2	NO	NO	all proteins are involved in 18S rRNA synthesis	
putative Hsp42-Gln1 complex	YDR171W; YPR035W	HSP42; GLN1	NO	NO		
putative Bud6-Yor304c-a complex	YLR319C; YOR304C-A	BUD6; YOR304C-A	NO	NO		
putative Skp1-Ypt52-Ymr258c complex	YDR328C; YKR014C; YMR258C	SKP1; YPT52; YMR258C	NO	NO	Skp1 and Ymr258c are known to interact	11283612
putative Bat1-Bat2 complex	YHR208W; YJR148W	BAT1; BAT2	NO	NO	Bat1, Bat2 encode for the mitochondrial and cytosolic branched-chain amino acid aminotransferases respectively	
putative Nfs1-Isd11 complex	YCL017C; YER048W-A	NFS1; ISD11	NO	NO		
putative Ser3-Ser33 isozyme complex	YER081W; YIL074C	SER3; SER33	NO	NO	Ser3 is an isozyme of Ser33	12525494
putative Slx5-Swa2 complex	YDL013W; YDR320C	SLX5; SWA2	NO	NO		
putative Yjl070c-Amd1 complex	YJL070C; YML035C	YJL070C; AMD1	NO	NO		
putative Yer071c-Aim21-Cap1-Cap2 complex	YER071C; YIR003W; YIL034C; YKL007W	TDA2; AIM21; CAP2; CAP1	NO	NO	Cap1 and Cap2 are known to form heterodimers	
putative Mob1-Dbf20 complex	YIL106W; YPR111W	MOB1; DBF20	NO	NO	Mob1 is known to form a kinase complex with Dbf2 which shares 80% sequence homology with Dbf20p	
putative Psy2-Rrd1 complex	YNL201C; YIL153W	PSY2; RRD1	NO	NO		
putative Nvj1-Tos4 complex	YHR195W; YLR183C	NVJ1; TOS4	NO	NO		
putative Ark1-Ste4 complex	YDR264C; YOR212W	AKR1; STE4	NO	NO	Akr1 acts as a negative regulator of the pheromone response pathway, potentially through Ste4p	8524293; 8649369
putative Sla2-Lsb3 complex	YNL243W; YFR024C-A	SLA2; LSB3	NO	NO		
putative Cyc3-Yat1 complex	YAL039C; YAR035W	CYC3; YAT1	NO	NO		
putative Uba1-Ydr415c complex	YKL210W; YDR415C	UBA1; YDR415C	NO	NO		
putative Las17-Sla1-Vrp1 complex	YLR337C; YBL007C; YOR181W	VRP1; SLA1; LAS17	NO	NO		
putative Ela1-Tys1 complex	YNL230C; YGR185C	ELA1; TYS1	NO	NO		
putative Dre2-Tah18 complex	YKR071C; YPR048W	DRE2; TAH18	NO	NO	Both Dre2 and Tah18 show synthetic lethal interactions with pol3-13 allele	
putative Kex2-Sil1 complex	YNL238W; YOL031C	KEX2; SIL1	NO	NO		
putative Ssl2-Yor352w complex	YIL143C; YOR352W	SSL2; YOR352W	NO	NO		
putative Tdh3-Pgk1-Eno2-Fba1-Pgm1 complex	YGR192C; YCR012W; YHR174W; YKL060C; YKL152C	TDH3; PGK1; ENO2; FBA1; GPM1	NO	NO	All proteins are involved in gluconeogenesis	
putative Cin8-Zwf1 complex	YEL061C; YNL241C	CIN8; ZWF1	NO	NO		
putative Pcm1-Mgs1 complex	YEL058W; YNL218W	PCM1; MGS1	NO	NO		
putative Yef1-Utr1 complex	YEL041W; YJR049C	YEF1; UTR1	NO	NO	both ATP-NAD kinases	
putative Ost1-Stt3 complex	YJL002C; YGL022W	OST1; STT3	NO	NO	Both proteins are part of the bigger oligosaccharyltransferase complex	
putative Osh2-Swh1 complex	YDL019C; YAR042W	OSH2; SWH1	NO	NO		
putative Sit4-Sap185-Rts3-Hrk1 complex	YDL047W; YJL098W; YGR161C; YOR267C	SIT4; SAP185; RTS3; HRK1	NO	NO	Sit4 and Sap185 are known to be in a complex with eachother	
putative Grh1-Fmp38 complex	YDR517W; YOR205C	GRH1; LRC5	NO	NO		
putative Tif1-Tif2 complex	YKR059W; YJL138C	TIF1; TIF2	NO	NO	Tif1 and Tif2 are identical	
putative Sah1-Caf16 complex	YER043C; YFL028C	SAH1; CAF16	NO	NO	Caf16 is a member of CCR4-NOT complex	
putative Bre1-Lge1 complex	YDL074C; YPL055C	BRE1; LGE1	NO	NO		
putative Fmc1-Atp12 complex	YIL098C; YJL180C	FMC1; ATP12	NO	NO	Fmc1 is thought to hel the folding-stability or functioning of At12p	
putative Fpr3-Ssb2 complex	YML074C; YNL209W	FPR3; SSB2	NO	NO		
putative Ptc7-Sec14 complex	YHR076W; YMR079W	PTC7; SEC14	NO	NO		
putative Faa4-Ygl082w complex	YGL082W; YMR246W	YGL082W; FAA4	NO	NO		
putative Ykl088w-Ppz1 complex	YKL088W; YML016C	CAB3; PPZ1	NO	NO		
putative Hmt1-Scd6-Psp2 complex	YBR034C; YPR129W; YML017W	HMT1; SCD6; PSP2	NO	NO	Scd6 (Lsm13p) associates with methyltransferases (such as Hmt1p)	
putative Eft1-Eft2 complex	YOR133W; YDR385W	EFT1; EFT2	NO	NO	Both Eft1 and Eft2 encode for Elongation factor 2	
putative Mnl1-Pdi1 complex	YHR204W; YCL043C	MNL1; PDI1	NO	NO	both proteins located in the ER lumen, Pdi1 involved in formation disulfide bonds for secretory and cell-surface proteins, Mnl1 involved in degradation of glycoproteins	
putative Nnf2-Yel043w complex	YEL043W; YGR089W	YEL043W; NNF2	NO	NO		
putative Yae1-Ynl260c complex	YJR067C; YNL260C	YAE1; YNL260C	NO	NO		
putative Erv46-Erv41-Ero1 complex	YAL042W; YML067C; YML130C	ERV46; ERV41; ERO1	NO	NO	Erv46 and Erv41 are known to be in the same complex	11157978
putative Sok1-Rtn1-Crp1-Ids2-Pep4 complex	YDR006C; YDR233C; YHR146W; YJL146W; YPL154C	SOK1; RTN1; CRP1; IDS2; PEP4	NO	NO		
putative Vac8-Nce102 complex	YEL013W; YPR149W	VAC8; NCE102	NO	NO		
putative Tma20-Tma22 complex	YER007C-A; YJR014W	TMA20; TMA22	NO	NO		
putative Wbp1-Swp1 complex	YEL002C; YMR149W	WBP1; SWP1	NO	NO	Both proteins are part of the bigger oligosaccharyltransferase complex	
putative Ubc4-Ufd4 complex	YBR082C; YKL010C	UBC4; UFD4	NO	NO		
putative Sfp1-Mrs6 complex	YLR403W; YOR370C	SFP1; MRS6	NO	NO		
putative Trm3-Fas1 complex	YDL112W; YKL182W	TRM3; FAS1	NO	NO		
putative Ste23-Mrn1 complex	YLR389C; YPL184C	STE23; MRN1	NO	NO		
putative Drn1-Dbr1 complex	YGR093W; YKL149C	DRN1; DBR1	NO	NO		
putative Yak1-Ypl247c complex	YJL141C; YPL247C	YAK1; YPL247C	NO	NO		
putative Fap1-Fpr1-Yil161w complex	YNL135C; YNL023C; YIL161W	FPR1; FAP1; YIL161W	NO	NO		
putative Crn1-Inp52-Bsp1 complex	YLR429W; YNL106C; YPR171W	CRN1; INP52; BSP1	NO	NO		
putative Uga1-Ndt80 complex	YGR019W; YHR124W	UGA1; NDT80	NO	NO		
putative Ptc6-Pro2 complex	YCR079W; YOR323C	PTC6; PRO2	NO	NO		
putative Tub3-Gcn1-Gcn20-Gfa1-Mae1-Sam1-Clu1 complex	YML124C; YGL195W; YFR009W; YKL104C; YKL029C; YLR180W; YMR012W	TUB3; GCN1; GCN20; GFA1; MAE1; SAM1; CLU1	NO	NO		
putative Pex5-Mmt1 complex	YDR244W; YMR177W	PEX5; MMT1	NO	NO		
putative Pcl8-Pho85 CDK-cyclin complex	YPL031C; YPL219W	PHO85; PCL8	NO	NO	Pcl8 is known to regulate glycogen synthase through interaction with Pho85p	9032248; 11602261
putative Mba1-Ste50 complex	YBR185C; YCL032W	MBA1; STE50	NO	NO		
putative Ura5-Ura10 isozyme complex	YML106W; YMR271C	URA5; URA10	NO	NO	major and mnior isozymes	
putative Pmr1-Psd1 complex	YGL167C; YNL169C	PMR1; PSD1	NO	NO		
putative Kem1-Gbp2-Sro9-Sbp1 complex	YGL173C; YCL011C; YCL037C; YHL034C	KEM1; GBP2; SRO9; SBP1	NO	NO		
putative Ipp1-Tus1-Ypl066w complex	YBR011C; YLR425W; YPL066W	IPP1; TUS1; YPL066W	NO	NO		
putative Ede1-Syp1 complex	YBL047C; YCR030C	EDE1; SYP1	NO	NO		
putative Pex14-Pex17 complex	YGL153W; YNL214W	PEX14; PEX17	NO	NO	Pex14 and Pex17 are known to associate with eachother but also include Pex13p, Pex5 and Pex7p	
putative Sum1-Rfm1 complex	YDR310C; YOR279C	SUM1; RFM1	NO	NO		
putative Ptc4-Ydr186c complex	YBR125C; YDR186C	PTC4; YDR186C	NO	NO		
putative Ybr137w-Sgt2-Mdy2-Yor164c complex	YBR137W; YOR007C; YOL111C; YOR164C	YBR137W; SGT2; MDY2; GET4	NO	NO	interaction between Mdy2 and YOR164c has been shown (16702403)	
putative Ygr071c-Vid22-Tbf1 complex	YGR071C; YLR373C; YPL128C	YGR071C; VID22; TBF1	NO	NO		
putative Yhb1-Aco1 complex	YGR234W; YLR304C	YHB1; ACO1	NO	NO		
putative Yjr136c-Ykl033w complex	YJR136C; YKL033W	TTI2; TTI1	NO	NO		
putative Lys20-Lys21 isozyme complex	YDL131W; YDL182W	LYS21; LYS20	NO	NO		
putative Nth1-Bmh1-Bmh2 complex	YDR001C; YDR099W; YER177W	NTH1; BMH2; BMH1	NO	NO	Bmh1 is the major isoform of Bmh2p	
putative Met13-Yml082w complex	YGL125W; YML082W	MET13; YML082W	NO	NO		
putative Pyc1-Pyc2 isozyme complex	YGL062W; YBR218C	PYC1; PYC2	NO	NO	Pyc2 is an isozyme of Pyc1, only double deletion shows phenotype	
putative Gir2-Rbg2 complex	YDR152W; YGR173W	GIR2; RBG2	NO	NO		
putative Yhr131c-Rsp5 complex	YHR131C; YER125W	YHR131C; RSP5	NO	NO		
putative Ptc3-Paa1 complex	YBL056W; YDR071C	PTC3; PAA1	NO	NO		
putative Aro3-Bcs1 complex	YDR035W; YDR375C	ARO3; BCS1	NO	NO		
putative Yor251c-Rev1 complex	YOR251C; YOR346W	TUM1; REV1	NO	NO		
putative Cmd1-Mlc1-Myo2-Myo1-Mlc2 complex	YBR109C; YGL106W; YOR326W; YHR023W; YPR188C	CMD1; MLC1; MYO2; MYO1; MLC2	NO	NO		
putative Efg1-Bud22 complex	YMR014W; YGR271C-A	BUD22; EFG1	NO	NO		
putative Hsp42-Sis1 complex	YDR171W; YNL007C	HSP42; SIS1	NO	NO		
putative Ygr017w-Vip1 complex	YGR017W; YLR410W	YGR017W; VIP1	NO	NO		
putative Ygr130c-Ymr031c complex	YGR130C; YMR031C	YGR130C; YMR031C	NO	NO		
putative Put1-Ymr315w complex	YLR142W; YMR315W	PUT1; YMR315W	NO	NO		
putative Crm1-Mir1-Erd2-Tub1-Gea2-Mtr10-Kap104 complex	YGR218W; YJR077C; YBL040C; YML085C; YEL022W; YOR160W; YBR017C	CRM1; MIR1; ERD2; TUB1; GEA2; MTR10; KAP104	NO	NO		
putative Kap95-Nup1 nuclear pore subcomplex	YLR347C; YOR098C	KAP95; NUP1	NO	NO	contains only part of the nuclear pore complex	
putative Emp24-Erv25-Erp3-Erp5 complex	YGL200C; YML012W; YDL018C; YHR110W	EMP24; ERV25; ERP3; ERP5	NO	NO	Erp3p, Erp5 have protein similarity with Emp24 and Erv25p	
putative Gdh1-Gdh3 isozyme complex	YOR375C; YAL062W	GDH1; GDH3	NO	NO		
putative Sas3-Nto1-Ylr455w complex	YBL052C; YPR031W; YLR455W	SAS3; NTO1; YLR455W	NO	NO	Sas3 and Nto1 are part of the NuA3 complex	
putative Cwc2-Spp382-Ntr2 complex	YDL209C; YLR424W; YKR022C	CWC2; SPP382; NTR2	NO	NO		
putative Heh2-Erg24 complex	YDR458C; YNL280C	HEH2; ERG24	NO	NO		
putative Sgn1-Ygr250c complex	YGR250C; YIR001C	YGR250C; SGN1	NO	NO		
putative Oca6-Oca5-Oca4-Oca3-Oca1-Oca2 complex	YDR067C; YHL029C; YCR095C; YNL032W; YNL099C; YNL056W	OCA6; OCA5; OCA4; SIW14; OCA1; OCA2	NO	NO		
putative Yll032c-Yml119w complex	YLL032C; YML119W	YLL032C; YML119W	NO	NO		
putative Map1-Ybr030w complex	YBR030W; YLR244C	RKM3; MAP1	NO	NO		
putative core TFIIH Tfb5-Tfb2 subcomplex	YDR079C-A; YPL122C	TFB5; TFB2	NO	NO		
putative Gsy1-Gsy2 complex	YLR258W; YFR015C	GSY2; GSY1	NO	NO	Gsy1 and Gsy2 are similar	
putative Ycp4-Rfs1-Pst2 complex	YCR004C; YBR052C; YDR032C	YCP4; RFS1; PST2	NO	NO	all proteins are members of the flavodoxin-like proteins	
putative Dhr2-Ubp10 complex	YKL078W; YNL186W	DHR2; UBP10	NO	NO		
putative Ats1-Kti11 complex	YAL020C; YBL071W-A	ATS1; KTI11	NO	NO		
putative Yer140w-Slp1 complex	YER140W; YOR154W	YER140W; SLP1	NO	NO		
putative Ipp1-Ack1-Rom2 complex	YBR011C; YDL203C; YLR371W	IPP1; ACK1; ROM2	NO	NO		
putative Ypk1-Ypk2 complex	YKL126W; YMR104C	YPK1; YPK2	NO	NO	Ypk1 and Ypk2 are functionally redundant	
putative Tao3-Yml081w complex	YIL129C; YML081W	TAO3; TDA9	NO	NO		
putative Hrr25-Ltv1-Rio2-Tsr1 complex	YKL143W; YDL060W; YPL204W; YNL207W	LTV1; TSR1; HRR25; RIO2	NO	NO		
putative Arx1-Rsa4-Sda1-Ipi3-Nsa2-Nog2-Bud20-Ipi1-Mdn1 complex	YDR101C; YCR072C; YGR245C; YNL182C; YER126C; YNR053C; YLR074C; YHR085W; YLR106C	ARX1; RSA4; SDA1; IPI3; NSA2; NOG2; BUD20; IPI1; MDN1	NO	NO	most proteins are associated with pre-60S ribosomal particles	
putative Hog1-Rck2 complex	YLR113W; YLR248W	HOG1; RCK2	NO	NO	Hog1 is known to phosphorylate Rck2p	11344302
putative Nup170-Nup53-Hms1 complex	YBL079W; YMR153W; YOR032C	NUP170; NUP53; HMS1	NO	NO		
putative Ade16-Ade17-Sol2 complex	YMR120C; YCR073W-A; YLR028C	ADE17; SOL2; ADE16	NO	NO	Ade17 and Ade17 encode isoforms	
putative Rgd1-Fyv8 complex	YBR260C; YGR196C	RGD1; FYV8	NO	NO		
putative Pet112-Ymr293c complex	YBL080C; YMR293C	PET112; HER2	NO	NO	petite formation, decreased metabolite accumulation	
putative Cul3-Yil001w complex	YGR003W; YIL001W	CUL3; YIL001W	NO	NO		
putative Paa1-Ptc2 complex	YDR071C; YER089C	PAA1; PTC2	NO	NO		
putative Ypt1-Dss4 complex	YFL038C; YPR017C	YPT1; DSS4	NO	NO	all proteins involved in post-Golgi vesicle mediated transport	
putative Nma2-Nma1 complex	YGR010W; YLR328W	NMA2; NMA1	NO	NO	both proteins are involved in the NAD salvage pathway	
putative Cia1-Yhr122w-Met18-Nar1 complex	YDR267C; YHR122W; YIL128W; YNL240C	CIA1; YHR122W; MET18; NAR1	NO	NO		
putative Ddi1-Pmt4 complex	YER143W; YJR143C	DDI1; PMT4	NO	NO		
putative Ygr283c-Idp3 complex	YGR283C; YNL009W	YGR283C; IDP3	NO	NO		
putative Abp1-Crn1 complex	YCR088W; YLR429W	ABP1; CRN1	NO	NO	Abp1 is an activator of the Arp2-3 complex, whereas Crn1 inhibits its function	
putative Met13-Met12 isozyme complex	YGL125W; YPL023C	MET13; MET12	NO	NO		
putative Boi2-Cdc24 complex	YAL041W; YER114C	CDC24; BOI2	NO	NO		
putative Fun19-Kap123 complex	YAL034C; YER110C	FUN19; KAP123	NO	NO		
putative Ygr283c-Ymr310c complex	YGR283C; YMR310C	YGR283C; YMR310C	NO	NO		
putative Trr1-Trr2 complex	YDR353W; YHR106W	TRR1; TRR2	NO	NO	Trr1 is part of the cytoplasmic thioredoxin system, Trr2 is part of the mitochondrial thioredoxin system (both thioredoxin reductases)	
putative Fbp26-Ylr345w complex	YJL155C; YLR345W	FBP26; YLR345W	NO	NO	Ylr345w show similarity to 6-phosphofructo-2-kinase-fructose-2,6-bisphosphatase enzymes	
putative Pck1-Eno1 complex	YBL105C; YGR254W	PKC1; ENO1	NO	NO		
putative Tdh1-Tdh2 isozyme complex	YJL052W; YJR009C	TDH1; TDH2	NO	NO		
putative Gdi1-Ypt6-Ypt1 complex	YER136W; YLR262C; YFL038C	GDI1; YPT6; YPT1	NO	NO	all proteins involved in post-Golgi vesicle mediated transport	
putative Bdh1-Bdh2 complex	YAL060W; YAL061W	BDH1; BDH2	NO	NO	BDH2 has 51% homology with BDH1, putative alcohol dehydrogenase	
putative Rps0a-Rps0b complex	YGR214W; YLR048W	RPS0A; RPS0B	NO	NO	Rps0a and Rps0b are nearly identical	
putative Ubp13-Yol087c complex	YBL067C; YOL087C	UBP13; DUF1	NO	NO		
putative Pol4-Rpn5 complex	YCR014C; YDL147W	POL4; RPN5	NO	NO		
putative Erg7-Erg27 complex	YHR072W; YLR100W	ERG7; ERG27	NO	NO	both proteins are involved in ergosterol biosynthesis	
putative Rrp7-Ifh1 complex	YCL031C; YLR223C	RRP7; IFH1	NO	NO		
putative Asn1-Asn2 isozyme complex	YGR124W; YPR145W	ASN2; ASN1	NO	NO		
putative Mdm10-Mpm1-Tom40-Yhm2 complex	YAL010C; YJL066C; YMR203W; YMR241W	MDM10; MPM1; TOM40; YHM2	NO	NO		
putative Ybt1-Dak1 complex	YLL048C; YML070W	YBT1; DAK1	NO	NO		
putative Cdc19-Pyk2 isozyme complex	YAL038W; YOR347C	CDC19; PYK2	NO	NO	Cdc19 and Pyk2 both encode pyruvate kinases and can compensate eachothers loss	
putative Pkh1-Mrp8-Pil1-Lsp1 complex	YDR490C; YKL142W; YGR086C; YPL004C	PKH1; MRP8; PIL1; LSP1	NO	NO	Pil1 and Lsp1 are known to be in the same complex (eiosome)	
putative Lsg1-Nmd3-Rei1 complex	YGL099W; YBR267W; YHR170W	LSG1; REI1; NMD3	NO	NO		
putative Taf8-Taf14-Taf2 TFIID subcomplex	YML114C; YPL129W; YCR042C	TAF8; TAF14; TAF2	NO	NO	All proteins are part of a bigger complex, TFIID	
putative Ssd1-Psy4-Pph3-Psy2 complex	YDR293C; YBL046W; YDR075W; YNL201C	SSD1; PSY4; PPH3; PSY2	NO	NO		
putative Rim1-Rad52 complex	YCR028C-A; YML032C	RIM1; RAD52	NO	NO		
putative Nqm1-Tal1 complex	YGR043C; YLR354C	NQM1; TAL1	NO	NO		
putative Vab2-Ydr357c-Ykl061w-YGL079w-Ynl086w complex	YDR357C; YKL061W; YEL005C; YGL079W; YNL086W	YDR357C; YKL061W; VAB2; YGL079W; YNL086W	NO	NO		
putative Kap123-Ypr174c complex	YER110C; YPR174C	KAP123; YPR174C	NO	NO		
putative Spe3-Spe4 complex	YLR146C; YPR069C	SPE4; SPE3	NO	NO	both proteins are part of the pantothenic acid biosynthesis pathway	11154694
putative Leu4-Leu9 isozyme complex	YNL104C; YOR108W	LEU4; LEU9	NO	NO		
putative Snf7-Vps4 complex	YLR025W; YPR173C	SNF7; VPS4	NO	NO	Vps4 is needed for dissociation of the ESCRT II complex (of which Snf7 is part of)	
putative Hmg1-Hmg2 isozyme complex	YLR450W; YML075C	HMG2; HMG1	NO	NO		
putative Oye2-Oye3 complex	YHR179W; YPL171C	OYE2; OYE3	NO	NO	Oye2 and Oye3 are homologous	
putative Glt1-Ylr257w complex	YDL171C; YLR257W	GLT1; YLR257W	NO	NO		
spliceosome	YGL120C; YBR065C; YJR050W; YAL032C; YDR364C; YGR278W; YCR063W; YMR213W; YDL209C; YDR416W; YLL036C; YLR117C; YPL151C; YPR101W; YGL128C; YLR424W	PRP43; ECM2; ISY1; PRP45; CDC40; CWC22; BUD31; CEF1; CWC2; SYF1; PRP19; CLF1; PRP46; SNT309; CWC23; SPP382	NO, not specific enough	NO	Different compositions around Ntc20 and Cef1 complexes are known, which overla to a large degree