PPI - IID Symbol 1 Symbol 2 PMID DBs Evidence Type Adipose Tissue Adrenal Gland Amygdala Bone Bone Marrow Brain Dorsal Root Ganglia Eye Heart Hindgut Hypothalamus Kidney Liver Lung Lymph Nodes Mammary Gland Midgut Neurons Ovary Pancreas Pituitary Gland Placenta Prostate Salivary Gland Skeletal Muscle Small Intestine Spleen Stomach Testes Uterus POR1 OTU1 22902402 biogrid exp RPL40B OTU1 22902402 biogrid exp SSB1 OTU1 22902402,16429126,19536198 biogrid,intact exp PDR5 OTU1 11957110 biogrid exp RPS0A OTU1 22902402 biogrid exp YEF3 OTU1 22902402 biogrid exp SAM1 OTU1 22902402 biogrid exp TMA19 OTU1 22902402 biogrid exp RPS31 OTU1 22902402 biogrid exp NAB2 OTU1 19840948 biogrid exp PDS1 OTU1 22072716 biogrid exp SPT23 OTU1 16427015 biogrid exp NOP1 OTU1 22902402 biogrid exp OTU1 COF1 22902402 biogrid exp RPS11B OTU1 22902402 biogrid exp RPL16A OTU1 22902402 biogrid exp GDH1 OTU1 22902402 biogrid exp OTU1 BFA1 16554755 intact exp HSC82 OTU1 22902402 biogrid exp FAS1 OTU1 22902402 biogrid exp OTU1 TSA2 22902402 biogrid exp PDB1 OTU1 22902402 biogrid exp SAH1 OTU1 22902402 biogrid exp OTU1 RPS15 22902402 biogrid exp MAM33 OTU1 i2d exp RPS4B OTU1 22902402 biogrid exp SSA2 OTU1 22902402,16429126 biogrid,intact exp MIR1 OTU1 22902402 biogrid exp OTU1 NOP56 22902402 biogrid exp RPL33A OTU1 22902402 biogrid exp HHF1, HHF2 OTU1 22902402,16429126 biogrid,intact exp PRC1 OTU1 25215493 intact exp PET9 OTU1 22902402 biogrid exp SSB2 OTU1 23332755,22902402 biogrid exp OTU1 NAF1 14690591 intact exp SSE1 OTU1 19536198 intact exp SES1 OTU1 22902402 biogrid exp RPS8B OTU1 22902402 biogrid exp HOM6 OTU1 22902402 biogrid exp PFK1 OTU1 22902402 biogrid exp RPS9B OTU1 22902402 biogrid exp RPL26A OTU1 22902402 biogrid exp RPL31A OTU1 22902402 biogrid exp OTU1 RPL17B 22902402 biogrid exp BMH2 OTU1 22902402 biogrid exp OTU1 LYS21 22902402 biogrid exp PSA1 OTU1 16429126 intact exp OTU1 HRD1 25215493 intact exp UBI4 OTU1 23827681,16427015,18270205 biogrid exp EFT1, EFT2 OTU1 22902402 biogrid exp SSA1 OTU1 22902402,19536198,23217712 biogrid,intact exp ILV5 OTU1 22902402 biogrid exp RPL15A OTU1 22902402 biogrid exp TSA1 OTU1 22902402 biogrid exp RPL3 OTU1 22902402 biogrid exp Putative uncharacterized protein YLR339C OTU1 11283351 i2d,mint,intact,dip exp RPL1B OTU1 22902402 biogrid exp RPS2 OTU1 22902402 biogrid exp OTU1 RPL13A 22902402 biogrid exp OTU1 PUF3 26493364 biogrid exp TKL1 OTU1 22902402 biogrid exp RPL16B OTU1 22902402 biogrid exp CDC6 OTU1 16429126 intact exp TEF1, TEF2 OTU1 16429126 intact exp SEC53 OTU1 22902402 biogrid exp RPL33B OTU1 22902402 biogrid exp DED81 OTU1 22902402 biogrid exp OTU1 OTU1 22902402 biogrid exp, ortho CDC48 OTU1 22902402,16427015,16429126,18270205,16554755,18719252, 23023127 biogrid,i2d,mint,intact exp, ortho, pred NPL4 OTU1 16427015, 23023127 biogrid exp, ortho, pred OTU1 UFD1 16427015, 23023127 biogrid exp, ortho, pred OTU1 UFD2 16427015,18719252, 23023127 biogrid,intact exp, pred DOA1 OTU1 16427015, 23023127 biogrid exp, pred SHP1 OTU1 16427015,18719252, 23023127 biogrid,i2d,intact exp, pred POL3 OTU1 ortho UBX7 OTU1 23023127 pred RAD23 OTU1 23023127 pred OTU1 SMT3 23023127 pred MPE1 OTU1 23023127 pred OTU1 UBP6 23023127 pred OTU1 UBX5 23023127 pred OTU1 UBI4 23023127 pred OTU1 DSK2 23023127 pred OTU1 UBX6 23023127 pred URM1 OTU1 23023127 pred OTU1 UBX3 23023127 pred OTU1 HUB1 23023127 pred ATG12 OTU1 23023127 pred

PPI - iRefIndex UniProt A UniProt B Method PMID Interaction Type Edge type Num Participants P10592 P43558 affinity chromatography technology 22902402 physical association X 2 P39954 P43558 affinity chromatography technology 22902402 physical association X 2 P26784 P43558 affinity chromatography technology 22902402 physical association X 2 P0CH08 P43558 affinity chromatography technology 22902402 physical association X 2 P0C2H8 P43558 affinity chromatography technology 22902402 physical association X 2 P05748 P43558 affinity chromatography technology 22902402 physical association X 2 P23641 P43558 affinity chromatography technology 22902402 physical association X 2 P05759 P43558 affinity chromatography technology 22902402 physical association X 2 P34730 P43558 affinity chromatography technology 22902402 physical association X 2 P41056 P43558 affinity chromatography technology 22902402 physical association X 2 W4YHN9 P43558 enzymatic study 22072716 direct interaction X 2 P53044 P43558 pull down 16427015 direct interaction X 2 P53044 P43558 affinity chromatography technology 16427015 physical association X 2 Q03048 P43558 affinity chromatography technology 22902402 physical association X 2 P34223 P43558 pull down 16427015 direct interaction X 2 P34223 P43558 affinity chromatography technology 16427015 physical association X 2 P34223 P43558 two hybrid 18719252 direct interaction X 2 P35210 P43558 affinity chromatography technology 16427015 physical association X 2 P33302 P43558 two hybrid 11957110 direct interaction X 2 P34760 P43558 affinity chromatography technology 22902402 physical association X 2 P0CX35 P43558 affinity chromatography technology 22902402 physical association X 2 P07284 P43558 affinity chromatography technology 22902402 physical association X 2 P07283 P43558 affinity chromatography technology 22902402 physical association X 2 P25694 P43558 pull down 18270205 direct interaction X 2 P25694 P43558 affinity chromatography technology 22902402 physical association X 2 P25694 P43558 two hybrid 16427015 direct interaction X 2 P25694 P43558 affinity chromatography technology 16554755 physical association X 2 P25694 P43558 pull down 16427015 direct interaction X 2 P54860 P43558 pull down 16427015 direct interaction X 2 P54860 P43558 affinity chromatography technology 16427015 physical association X 2 P25694 P43558 affinity chromatography technology 16427015 physical association X 2 P54860 P43558 two hybrid 18719252 direct interaction X 2 P25694 P43558 two hybrid 18719252 direct interaction X 2 P05743 P43558 affinity chromatography technology 22902402 physical association X 2 P40150 P43558 affinity chromatography technology 22902402 physical association X 2 P40150 P43558 biochemical 23332755 association X 2 P14126 P43558 affinity chromatography technology 22902402 physical association X 2 P05744 P43558 affinity chromatography technology 22902402 physical association X 2 P23254 P43558 affinity chromatography technology 22902402 physical association X 2 P43558 P43558 affinity chromatography technology 22902402 physical association X 2 P10659 P43558 affinity chromatography technology 22902402 physical association X 2 P55072 P43558 x-ray crystallography 24610782 association X 2 P55072 P43558 x-ray crystallography 24610782 association X 2 P55072 P43558 pull down 25084388 direct interaction X 2 P55072 P43558 x-ray crystallography 25084388 association X 2 P0CX47 P43558 affinity chromatography technology 22902402 physical association X 2 Q01855 P43558 affinity chromatography technology 22902402 physical association X 2 P36037 P43558 two hybrid 16427015 direct interaction X 2 P36037 P43558 pull down 16427015 direct interaction X 2 P36037 P43558 affinity chromatography technology 16427015 physical association X 2 P18239 P43558 affinity chromatography technology 22902402 physical association X 2 P16521 P43558 affinity chromatography technology 22902402 physical association X 2 P33755 P43558 pull down 16427015 direct interaction X 2 P33755 P43558 affinity chromatography technology 16427015 physical association X 2 Q12122 P43558 affinity chromatography technology 22902402 physical association X 2 P06168 P43558 affinity chromatography technology 22902402 physical association X 2 P46990 P43558 affinity chromatography technology 22902402 physical association X 2 P35691 P43558 affinity chromatography technology 22902402 physical association X 2 P31116 P43558 affinity chromatography technology 22902402 physical association X 2 P11484 P43558 affinity chromatography technology 22902402 physical association X 2 P15108 P43558 affinity chromatography technology 22902402 physical association X 2 P32905 P43558 affinity chromatography technology 22902402 physical association X 2 P16861 P43558 affinity chromatography technology 22902402 physical association X 2 P0CG63 P43558 pull down 18270205 direct interaction X 2 P0CG63 P43558 x-ray crystallography 18270205 association X 2 P0CG63 P43558 affinity chromatography technology 23749301 physical association X 2 P0CG63 P43558 enzymatic study 16427015 direct interaction X 2 P0CG63 P43558 enzymatic study 23827681 direct interaction X 2 P0CG63 P43558 affinity chromatography technology 23793018 physical association X 2 P0CG63 P43558 affinity chromatography technology 12872131 physical association X 2 P0CG63 P43558 affinity chromatography technology 22106047 physical association X 2 Q04120 P43558 affinity chromatography technology 22902402 physical association X 2 P32324 P43558 affinity chromatography technology 22902402 physical association X 2 P07262 P43558 affinity chromatography technology 22902402 physical association X 2 Q12460 P43558 affinity chromatography technology 22902402 physical association X 2 P32473 P43558 affinity chromatography technology 22902402 physical association X 2 P38707 P43558 affinity chromatography technology 22902402 physical association X 2 P0CX39 P43558 affinity chromatography technology 22902402 physical association X 2 P40316 P43558 enzymatic study 22072716 direct interaction X 2 P04840 P43558 affinity chromatography technology 22902402 physical association X 2 P0CX43 P43558 affinity chromatography technology 22902402 physical association X 2 Q12690 P43558 affinity chromatography technology 22902402 physical association X 2 P43558 P15646 affinity chromatography technology 22902402 physical association X 2 P10591 P43558 affinity chromatography technology 22902402 physical association X 2 P10591 P43558 affinity chromatography technology 19536198 physical association X 2 P10591 P43558 affinity chromatography technology 19536198 physical association X 2 P02309 P43558 affinity chromatography technology 22902402 physical association X 2 P25443 P43558 affinity chromatography technology 22902402 physical association X 2 P07149 P43558 affinity chromatography technology 22902402 physical association X 2 P05755 P43558 affinity chromatography technology 22902402 physical association X 2 P26785 P43558 affinity chromatography technology 22902402 physical association X 2 O94085 P43558 two hybrid pooling approach 11283351 physical association X 2 P62987 P43558 cleavage assay 21245344 direct interaction X 2 P43558 pull down 23217712 association C 317 P43558 inferred by author 16554755 association C 22 P32589 P43558 tandem affinity purification 19536198 association X 2 P34223 P43558 two hybrid 18719252 physical association X 2 P53919 P43558 two hybrid array 14690591 physical association X 2 P25694 P43558 tandem affinity purification 16554755 physical association X 2 P25694 P43558 tandem affinity purification 16554755 physical association X 2 P25694 P43558 tandem affinity purification 16554755 physical association X 2 P54860 P43558 two hybrid 18719252 physical association X 2 P25694 P43558 two hybrid 18719252 physical association X 2 P00729 P43558 deubiquitinase assay 25215493 deubiquitination reaction X 2 P43558 tandem affinity purification 16429126 association C 8 Q08109 P43558 deubiquitinase assay 25215493 deubiquitination reaction X 2 O94085 P43558 two hybrid fragment pooling approach 11283351 physical association X 2 P11484 P43558 tandem affinity purification 19536198 association X 2 P10591 P43558 tandem affinity purification 19536198 association X 2 P10591 P43558 tandem affinity purification 19536198 association X 2 O94085 P43558 two hybrid 11283351 - X 2

PPI - HINT Gene A Gene B PMID Method Quality O94085 OTU1 11283351,11283351,11283351 0018,0399,0398 HT PRC1 OTU1 25215493 0998 LC UBI4 OTU1 18270205,16427015,18270205,23827681 0114,0415,0096,0415 LC CDC48 OTU1 18719252,16427015,16427015,16427015 0018,0004,0018,0096 HT,LC PDR5 OTU1 11957110 0018 LC SAS3 OTU1 18719252 0018 HT DOA1 OTU1 16427015,16427015,16427015 0004,0018,0096 LC SSB2 OTU1 23332755 0401 LC PDS1 OTU1 22072716 0415 LC OTU1 OTU1 18270205 0114 LC OTU1 NAF1 14690591 0397 LC OTU1 UFD2 18719252 0018 HT OTU1 HRD1 25215493 0998 LC HHF1|HHF2 OTU1 16429126,22902402 0676,0004 HT,LC TEF1|TEF2 OTU1 16429126 0676 HT POR1 OTU1 22902402 0004 LC RPL26A OTU1 22902402 0004 LC RPL33A OTU1 22902402 0004 LC RPL15A OTU1 22902402 0004 LC RPS9B OTU1 22902402 0004 LC RPS31 OTU1 22902402 0004 LC ILV5 OTU1 22902402 0004 LC FAS1 OTU1 22902402 0004 LC GDH1 OTU1 22902402 0004 LC SEC53 OTU1 22902402 0004 LC SES1 OTU1 22902402 0004 LC CDC6 OTU1 16429126 0676 HT RPL31A OTU1 22902402 0004 LC UBI4 OTU1 18270205,18270205,22106047 0114,0096,0004 LC RPL40B OTU1 22902402 0004 LC RPS4B OTU1 22902402 0004 LC RPS8B OTU1 22902402 0004 LC RPL1B OTU1 22902402 0004 LC RPS11B OTU1 22902402 0004 LC SSA1 OTU1 19536198,23217712,22902402,19536198 0004,0096,0004,0676 HT,LC SSA2 OTU1 16429126,22902402 0676,0004 HT,LC SAM1 OTU1 22902402 0004 LC SSB1 OTU1 19536198,16429126,22902402 0676,0676,0004 HT,LC RPL3 OTU1 22902402 0004 LC HSC82 OTU1 22902402 0004 LC NOP1 OTU1 22902402 0004 LC YEF3 OTU1 22902402 0004 LC PFK1 OTU1 22902402 0004 LC PET9 OTU1 22902402 0004 LC TKL1 OTU1 22902402 0004 LC MIR1 OTU1 22902402 0004 LC RPS2 OTU1 22902402 0004 LC CDC48 OTU1 16554755,16427015,16429126,16427015,16427015,22902402,18270205,16554755 0004,0004,0676,0018,0096,0004,0096,0676 HT,LC RPL16A OTU1 22902402 0004 LC RPL16B OTU1 22902402 0004 LC HOM6 OTU1 22902402 0004 LC EFT1|EFT2 OTU1 22902402 0004 LC PDB1 OTU1 22902402 0004 LC NAB2 OTU1 19840948 0004 LC SSE1 OTU1 19536198 0676 HT RPS0A OTU1 22902402 0004 LC NPL4 OTU1 16427015,16427015 0096,0004 LC SAS3 OTU1 16427015,16427015 0096,0004 LC BMH2 OTU1 22902402 0004 LC TSA1 OTU1 22902402 0004 LC SPT23 OTU1 16427015 0004 LC TMA19 OTU1 22902402 0004 LC DOA1 OTU1 16427015,16427015,16427015 0004,0018,0096 LC DED81 OTU1 22902402 0004 LC SAH1 OTU1 22902402 0004 LC SSB2 OTU1 23332755,22902402 0401,0004 LC RPL33B OTU1 22902402 0004 LC PSA1 OTU1 16429126 0676 HT OTU1 OTU1 22902402 0004 LC OTU1 RPL17B 22902402 0004 LC OTU1 BFA1 16554755 0363 HT OTU1 UFD1 16427015,16427015 0096,0004 LC OTU1 UFD2 16427015,16427015 0096,0004 LC OTU1 RPS15 22902402 0004 LC OTU1 COF1 22902402 0004 LC OTU1 TSA2 22902402 0004 LC OTU1 LYS21 22902402 0004 LC OTU1 NOP56 22902402 0004 LC OTU1 RPL13A 22902402 0004 LC

PPI - Mentha Protein A Protein B Gene A Gene B Score PMID P43558 P25694 OTU1 CDC48 0.814 22902402,18270205,16427015,16429126,18719252,16554755 P43558 P11484 OTU1 SSB1 0.332 22902402,19536198,16429126 P43558 P10592 OTU1 SSA2 0.236 16429126,22902402 P43558 P02309 OTU1 HHF2 0.236 16429126,22902402 P43558 P34223 OTU1 SHP1 0.332 18719252 P43558 P10591 OTU1 SSA1 0.49 22902402,23217712,19536198 P43558 P0CG63 OTU1 UBI4 0.772 18270205,16427015,23827681 P43558 P32505 OTU1 NAB2 0.126 19840948 P43558 P40150 OTU1 SSB2 0.236 22902402,23332755 Q01855 P43558 RPS15 OTU1 0.126 22902402 Q03048 P43558 COF1 OTU1 0.126 22902402 Q04120 P43558 TSA2 OTU1 0.126 22902402 Q08109 P43558 HRD1 OTU1 0.033 25215493 Q12122 P43558 LYS21 OTU1 0.126 22902402 Q12460 P43558 NOP56 OTU1 0.126 22902402 Q12690 P43558 RPL13A OTU1 0.126 22902402 P53919 P43558 NAF1 OTU1 0.126 14690591 P43558 P39954 OTU1 SAH1 0.126 22902402 P43558 P34760 OTU1 TSA1 0.126 22902402 P43558 P31116 OTU1 HOM6 0.126 22902402 P43558 P15646 OTU1 NOP1 0.126 22902402 P43558 P10659 OTU1 SAM1 0.126 22902402 P43558 P0CX44 OTU1 RPL1B 0.126 22902402 P43558 P0CX40 OTU1 RPS8B 0.126 22902402 P43558 P0C2H8 OTU1 RPL31A 0.126 22902402 P46990 P43558 RPL17B OTU1 0.126 22902402 P43558 P34730 OTU1 BMH2 0.126 22902402 P43558 P07149 OTU1 FAS1 0.126 22902402 P43558 O94085 OTU1 O94085 0.21 11283351 P43558 P32905 OTU1 RPS0A 0.126 22902402 P43558 P32589 OTU1 SSE1 0.126 19536198 P43558 P26785 OTU1 RPL16B 0.126 22902402 P43558 P05759 OTU1 RPS31 0.126 22902402 P47113 P43558 BFA1 OTU1 0.126 16554755 P43558 P15108 OTU1 HSC82 0.126 22902402 P43558 P0CX43 OTU1 RPL1A 0.126 22902402 P43558 P06168 OTU1 ILV5 0.126 22902402 P43558 P05755 OTU1 RPS9B 0.126 22902402 P43558 P14126 OTU1 RPL3 0.126 22902402 P43558 P09119 OTU1 CDC6 0.126 16429126 P43558 P07262 OTU1 GDH1 0.126 22902402 P43558 P07284 OTU1 SES1 0.126 22902402 P43558 P07283 OTU1 SEC53 0.126 22902402 P55072 P43558 VCP OTU1 0.772 24610782,25084388 P43558 P38707 OTU1 DED81 0.126 22902402 P43558 P35691 OTU1 TMA19 0.126 22902402 P43558 P26784 OTU1 RPL16A 0.126 22902402 P43558 P05748 OTU1 RPL15A 0.126 22902402 P43558 P0CX47 OTU1 RPS11A 0.126 22902402 P43558 P0CX39 OTU1 RPS8A 0.126 22902402 P43558 P23641 OTU1 MIR1 0.126 22902402 P43558 P23254 OTU1 TKL1 0.126 22902402 P43558 P18239 OTU1 PET9 0.126 22902402 P43558 P0CH08 OTU1 RPL40A 0.126 22902402 P43558 P00729 OTU1 PRC1 0.033 25215493 P54860 P43558 UFD2 OTU1 0.332 18719252 P43558 P43558 OTU1 OTU1 0.155 22902402 P43558 P02994 OTU1 TEF2 0.126 16429126 P43558 P36037 OTU1 DOA1 0.309 16427015 P43558 P32473 OTU1 PDB1 0.126 22902402 P43558 P16521 OTU1 YEF3 0.126 22902402 P43558 P05744 OTU1 RPL33A 0.126 22902402 P43558 P41940 OTU1 PSA1 0.126 16429126 P43558 P41056 OTU1 RPL33B 0.126 22902402 P43558 P40316 OTU1 PDS1 0.309 22072716 P43558 P32324 OTU1 EFT2 0.126 22902402 P43558 P0CX36 OTU1 RPS4B 0.126 22902402 P43558 P0CX35 OTU1 RPS4A 0.126 22902402 P43558 P25443 OTU1 RPS2 0.126 22902402 P43558 P16861 OTU1 PFK1 0.126 22902402 P43558 P0CH09 OTU1 RPL40B 0.126 22902402 P43558 P04840 OTU1 POR1 0.126 22902402 P43558 P0CX48 OTU1 RPS11B 0.126 22902402 P43558 P05743 OTU1 RPL26A 0.126 22902402 Q07807 P43558 PUF3 OTU1 0.126