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 BIM1 UFD1 18832349 biogrid exp UFD1 PWWP domain-containing protein YLR455W i2d exp SPC42 UFD1 17634282 biogrid exp RPL18B UFD1 23358411 biogrid exp KAR9 UFD1 18832349 biogrid exp UFD1 ELG1 21869594 biogrid exp UFD1 PBP1 15121841 biogrid exp BBC1 UFD1 11743162 biogrid,i2d,mint,intact,dip exp PRC1 UFD1 16179952 intact exp BNI1 UFD1 16429126 intact exp HMG2 UFD1 16179952 biogrid,intact exp BFA1 UFD1 16554755 intact exp UFD1 RQC2 23178123 biogrid,intact exp RPS27A UFD1 12847084 biogrid exp RAD52 UFD1 23624404 biogrid exp UFD1 RQC1 23178123 biogrid,intact exp SSA2 UFD1 16429126 intact exp NDC80 UFD1 17634282 biogrid exp UFD1 NSE5 14690591 biogrid,i2d,intact exp VMA10 UFD1 11283351 i2d,mint,intact,dip exp SCH9 UFD1 i2d exp UFD1 PUF3 26493364 biogrid exp NDT80 UFD1 16554755 biogrid,i2d,mint,intact exp SPT23 UFD1 16427015 biogrid exp NPL4 UFD1 25215493,16429126,21211725,11283351,11598205,16554755,17289586,11805826,16179952,21070972,22940862,11733065,10688190, 23023127 biogrid,i2d,mint,intact,dip exp, ortho, pred OTU1 UFD1 16427015, 23023127 biogrid exp, ortho, pred CDC48 UFD1 15652483,25215493,16873066,16429126,21148305,21211725,21896481,16554755,11805826,16427015,16179952,22940862,11733065,15200949, 23023127 biogrid,i2d,mint,intact,dip exp, ortho, pred UFD1 UFD1 11805826,22940862, 23023127 biogrid,mint,intact exp, pred UFD1 FMP40 10688190, 23023127 biogrid,i2d,mint,intact,dip exp, pred UFD1 UBX2 16179952,16873066,22615397,18467557,21211725,23793018, 23023127 biogrid,i2d,mint,intact exp, pred DOA1 UFD1 16427015, 23023127 biogrid exp, pred PAP1 UFD1 9236779, 23023127 biogrid,i2d,dip exp, pred UFD1 SMT3 15590687, 23023127 biogrid exp, pred UFD1 UBX5 21211725, 23023127 biogrid,i2d exp, pred UFD1 HRD1 25215493,16179952, 23023127 biogrid,intact exp, pred UFD1 PIN3 11743162, 23023127 biogrid,i2d,mint,intact,dip exp, pred UBA2 UFD1 9236779, 23023127 biogrid,i2d,dip exp, pred SSM4 UFD1 16179952, 23023127 biogrid,intact exp, pred UFD1 UFD2 16427015,21211725, 23023127 biogrid,i2d exp, pred DER1 UFD1 16179952,18407841, 23023127 biogrid,mint,intact exp, pred UFD1 DFM1 18407841, 23023127 biogrid,mint,intact exp, pred SRV2 UFD1 ortho GRS1 UFD1 ortho DID4 UFD1 ortho MAD2 UFD1 ortho RPN1 UFD1 ortho HBS1 UFD1 ortho SHP1 UFD1 ortho DPH5 UFD1 ortho UFD1 RPN8 ortho STI1 UFD1 ortho GLE2 UFD1 ortho EMW1 UFD1 ortho UFD1 PRP43 ortho RAD23 UFD1 ortho RPT3 UFD1 23023127 pred PUP1 UFD1 23023127 pred UFD1 UBI4 23023127 pred

PPI - iRefIndex UniProt A UniProt B Method PMID Interaction Type Edge type Num Participants P53044 - 11805826 - C 9 P53044 - 16179952 - C 4 P53044 - 16179952 - C 4 P53044 - 15200949 - C 6 Q08968 P53044 - 10688190 - X 2 P53044 Q03718 - 14690591 - X 2 P29468 P53044 - 9236779 - X 2 P33755 P53044 - 10688190 - X 2 P33755 P53044 - 11283351 - X 2 P53044 - 16179952 - C 4 P53044 - 16179952 - C 4 P53044 - 11805826 - C 4 P53044 - 16179952 - C 4 P53044 - 11805826 - C 3 Q06449 P53044 - 11743162 - X 2 P52488 P53044 - 9236779 - X 2 P48836 P53044 - 11283351 - X 2 P47068 P53044 - 11743162 - X 2 Q12532 P53044 affinity chromatography technology 23178123 physical association X 2 Q08109 P53044 affinity chromatography technology 16179952 physical association X 2 P40013 P53044 two hybrid 18832349 direct interaction X 2 Q06682 P53044 affinity chromatography technology 21211725 physical association X 2 Q06682 P53044 affinity chromatography technology 21211725 physical association X 2 P12684 P53044 affinity chromatography technology 16179952 physical association X 2 P38307 P53044 affinity chromatography technology 16179952 physical association X 2 P38307 P53044 affinity chromatography technology 18407841 physical association X 2 P38307 P53044 affinity chromatography technology 18407841 physical association X 2 P35997 P53044 affinity chromatography technology 12847084 physical association X 2 Q08968 P53044 two hybrid 10688190 direct interaction X 2 P32526 P53044 two hybrid 18832349 direct interaction X 2 P40318 P53044 affinity chromatography technology 16179952 physical association X 2 P40460 P53044 two hybrid 17634282 direct interaction X 2 P53044 Q05468 affinity chromatography technology 23178123 physical association X 2 P53044 P43558 pull down 16427015 direct interaction X 2 P53044 P43558 affinity chromatography technology 16427015 physical association X 2 P53044 Q03718 two hybrid 14690591 direct interaction X 2 Q12050 P53044 two hybrid 21869594 direct interaction X 2 P54860 P53044 biochemical 16427015 association X 2 P54860 P53044 affinity chromatography technology 16427015 physical association X 2 P54860 P53044 affinity chromatography technology 21211725 physical association X 2 P29468 P53044 two hybrid 9236779 direct interaction X 2 P29468 P53044 pull down 9236779 direct interaction X 2 P36094 P53044 two hybrid 17634282 direct interaction X 2 P33755 P53044 affinity chromatography technology 22940862 physical association X 2 P33755 P53044 affinity chromatography technology 11733065 physical association X 2 P33755 P53044 affinity chromatography technology 11598205 physical association X 2 P33755 P53044 pull down 17289586 direct interaction X 2 P33755 P53044 affinity chromatography technology 16554755 physical association X 2 P33755 P53044 affinity chromatography technology 16429126 physical association X 2 P33755 P53044 affinity chromatography technology 16429126 physical association X 2 P33755 P53044 affinity chromatography technology 16179952 physical association X 2 P33755 P53044 affinity chromatography technology 16179952 physical association X 2 P33755 P53044 affinity chromatography technology 17200106 physical association X 2 P33755 P53044 two hybrid 11283351 direct interaction X 2 P33755 P53044 two hybrid 11283351 direct interaction X 2 P33755 P53044 affinity chromatography technology 21070972 physical association X 2 P33755 P53044 affinity chromatography technology 21211725 physical association X 2 P33755 P53044 affinity chromatography technology 21211725 physical association X 2 P33755 P53044 affinity chromatography technology 11805826 physical association X 2 P33755 P53044 affinity chromatography technology 11805826 physical association X 2 P33755 P53044 two hybrid 10688190 direct interaction X 2 Q04228 P53044 affinity chromatography technology 23793018 physical association X 2 Q04228 P53044 affinity chromatography technology 16179952 physical association X 2 Q04228 P53044 affinity chromatography technology 16179952 physical association X 2 Q04228 P53044 protein complementation assay 18467557 direct interaction X 2 Q04228 P53044 affinity chromatography technology 21211725 physical association X 2 Q04228 P53044 protein complementation assay 22615397 direct interaction X 2 Q06449 P53044 two hybrid 11743162 direct interaction X 2 Q12743 P53044 affinity chromatography technology 18407841 physical association X 2 P52488 P53044 two hybrid 9236779 direct interaction X 2 P0CG63 P53044 affinity chromatography technology 23749301 physical association X 2 P0CG63 P53044 affinity chromatography technology 23793018 physical association X 2 P0CG63 P53044 affinity chromatography technology 12872131 physical association X 2 P0CG63 P53044 affinity chromatography technology 21427232 physical association X 2 P06778 P53044 affinity chromatography technology 23624404 physical association X 2 P06778 P53044 affinity chromatography technology 23624404 physical association X 2 P53044 P53044 affinity chromatography technology 22940862 physical association X 2 P53297 P53044 two hybrid 15121841 direct interaction X 2 Q12306 P53044 two hybrid 15590687 direct interaction X 2 Q12306 P53044 affinity chromatography technology 15590687 physical association X 2 P35210 P53044 affinity chromatography technology 16427015 physical association X 2 P25694 P53044 affinity chromatography technology 22940862 physical association X 2 P25694 P53044 affinity chromatography technology 11733065 physical association X 2 P25694 P53044 affinity chromatography technology 15200949 physical association X 2 P25694 P53044 affinity chromatography technology 15652483 physical association X 2 P25694 P53044 pull down 16427015 direct interaction X 2 P25694 P53044 pull down 16427015 direct interaction X 2 P25694 P53044 affinity chromatography technology 16554755 physical association X 2 P25694 P53044 affinity chromatography technology 16429126 physical association X 2 P25694 P53044 affinity chromatography technology 16429126 physical association X 2 P25694 P53044 affinity chromatography technology 16179952 physical association X 2 P25694 P53044 affinity chromatography technology 16179952 physical association X 2 P25694 P53044 affinity chromatography technology 17200106 physical association X 2 P25694 P53044 affinity chromatography technology 21211725 physical association X 2 P25694 P53044 affinity chromatography technology 21211725 physical association X 2 P25694 P53044 affinity chromatography technology 11805826 physical association X 2 P25694 P53044 affinity chromatography technology 11805826 physical association X 2 P25694 P53044 affinity chromatography technology 21148305 physical association X 2 P25694 P53044 affinity chromatography technology 21896481 physical association X 2 P0CX49 P53044 affinity chromatography technology 23358411 physical association X 2 P38830 P53044 affinity chromatography technology 16554755 physical association X 2 P47068 P53044 two hybrid 11743162 direct interaction X 2 P36037 P53044 biochemical 16427015 association X 2 P36037 P53044 affinity chromatography technology 16427015 physical association X 2 P53044 tandem affinity purification 11805826 - C 9 P53044 inferred by author 11805826 physical association C 14 Q08968 P53044 two hybrid 10688190 physical association X 2 P29468 P53044 coimmunoprecipitation 9236779 physical association X 2 P29468 P53044 two hybrid 9236779 physical association X 2 P33755 P53044 coimmunoprecipitation 11733065 physical association X 2 P33755 P53044 two hybrid pooling approach 11283351 physical association X 2 P33755 P53044 two hybrid pooling approach 11283351 physical association X 2 P33755 P53044 two hybrid 10688190 physical association X 2 P33755 P53044 tandem affinity purification 11805826 physical association X 2 P33755 P53044 tandem affinity purification 11805826 physical association X 2 P53044 tandem affinity purification 11805826 - C 4 P53044 tandem affinity purification 11805826 - C 3 Q06449 P53044 two hybrid 11743162 physical association X 2 P52488 P53044 coimmunoprecipitation 9236779 physical association X 2 P52488 P53044 two hybrid 9236779 physical association X 2 P53044 P63048 nuclear magnetic resonance 16004872 direct interaction X 2 P25694 P53044 two hybrid 11733065 physical association X 2 P25694 P53044 tandem affinity purification 21807993 physical association X 2 P25694 P53044 coimmunoprecipitation 11733065 physical association X 2 P25694 P53044 tandem affinity purification 11805826 physical association X 2 P25694 P53044 tandem affinity purification 11805826 physical association X 2 P25694 P53044 pull down 21807993 physical association X 2 P48836 P53044 two hybrid pooling approach 11283351 physical association X 2 P47068 P53044 two hybrid 11743162 physical association X 2 P53044 anti tag coimmunoprecipitation 16179952 association C 4 P53044 anti bait coimmunoprecipitation 16179952 association C 4 P53044 anti bait coimmunoprecipitation 16179952 association C 4 P53044 tandem affinity purification 11805826 association C 4 P53044 tandem affinity purification 11805826 association C 4 P53044 tandem affinity purification 16429126 association C 19 P53044 anti tag coimmunoprecipitation 23178123 association C 21 P53044 anti tag coimmunoprecipitation 23178123 association C 21 P53044 molecular sieving 25215493 physical association C 3 P53044 molecular sieving 25215493 physical association C 3 P53044 anti tag coimmunoprecipitation 23178123 association C 8 P53044 anti tag coimmunoprecipitation 16179952 association C 4 P53044 tandem affinity purification 11805826 association C 10 P53044 tandem affinity purification 16429126 association C 4 P53044 pull down 25215493 association C 3 P53044 inferred by author 16554755 association C 22 P38307 P53044 anti tag coimmunoprecipitation 18407841 physical association X 2 Q08968 P53044 two hybrid 10688190 physical association X 2 P53044 Q03718 two hybrid array 14690591 physical association X 2 P33755 P53044 two hybrid 10688190 physical association X 2 P33755 P53044 two hybrid fragment pooling approach 11283351 physical association X 2 P33755 P53044 two hybrid fragment pooling approach 11283351 physical association X 2 P33755 P53044 tandem affinity purification 16554755 physical association X 2 P53044 anti tag coimmunoprecipitation 18407841 association C 9 P53044 tandem affinity purification 16873066 association C 10 P53044 tandem affinity purification 16873066 association C 6 P53044 pull down 25215493 association C 4 P53044 anti tag coimmunoprecipitation 16179952 association C 4 P53044 anti tag coimmunoprecipitation 16179952 association C 4 P53044 anti tag coimmunoprecipitation 16179952 association C 3 P53044 tandem affinity purification 11805826 association C 5 P53044 anti tag coimmunoprecipitation 16179952 association C 4 P53044 molecular sieving 25215493 physical association C 4 P53044 molecular sieving 25215493 physical association C 4 P53044 molecular sieving 25215493 physical association C 3 P53044 molecular sieving 25215493 physical association C 3 P53044 anti tag coimmunoprecipitation 16179952 association C 4 P53044 tandem affinity purification 16429126 association C 6 P53044 pull down 25215493 association C 5 P53044 inferred by author 16429126 physical association C 9 Q04228 P53044 dihydrofolate reductase reconstruction 18467557 physical association X 2 Q04228 P53044 dihydrofolate reductase reconstruction 18467557 physical association X 2 Q06449 P53044 two hybrid 11743162 physical association X 2 Q12743 P53044 anti tag coimmunoprecipitation 18407841 physical association X 2 P25694 P53044 tandem affinity purification 16554755 physical association X 2 P25694 P53044 tandem affinity purification 16554755 physical association X 2 P25694 P53044 tandem affinity purification 16554755 physical association X 2 P25694 P53044 tandem affinity purification 16554755 physical association X 2 P25694 P53044 tandem affinity purification 16554755 physical association X 2 P25694 P53044 tandem affinity purification 16554755 physical association X 2 P48836 P53044 two hybrid fragment pooling approach 11283351 physical association X 2 P38830 P53044 tandem affinity purification 16554755 physical association X 2 P47068 P53044 two hybrid 11743162 physical association X 2 P53044 mass spectrometry studies of complexes 11805826 - C 19 P53044 mass spectrometry studies of complexes 11805826 - C 19 Q08968 P53044 two hybrid 10688190 - X 2 P29468 P53044 two hybrid 9236779 - X 2 P33755 P53044 two hybrid 10688190 - X 2 P33755 P53044 two hybrid 11283351 - X 2 P33755 P53044 two hybrid 11283351 - X 2 Q06449 P53044 two hybrid 11743162 - X 2 P52488 P53044 two hybrid 9236779 - X 2 P48836 P53044 two hybrid 11283351 - X 2 P47068 P53044 two hybrid 11743162 - X 2

PPI - HINT Gene A Gene B PMID Method Quality CDC48 UFD1 25215493,11733065,11733065,11733065 0071,0004,0018,0019 LC PAP1 UFD1 9236779,9236779,9236779,9236779 0019,0004,0018,0096 LC KAR9 UFD1 18832349 0018 LC NPL4 UFD1 25215493,11733065,11283351,10688190,11733065,11283351,10688190,11283351 0071,0004,0398,0397,0019,0399,0018,0018 LC,HT DOA1 UFD1 16427015,16427015 0401,0004 LC SPC42 UFD1 17634282 0018 HT BIM1 UFD1 18832349 0018 LC NDC80 UFD1 17634282 0018 HT BBC1 UFD1 11743162,11743162 0397,0018 HT VMA10 UFD1 11283351,11283351,11283351 0018,0399,0398 HT UBA2 UFD1 9236779,9236779 0019,0018 LC UFD1 PBP1 15121841 0018 LC UFD1 UFD2 16427015,16427015 0401,0004 LC UFD1 NSE5 14690591,14690591 0018,0397 LC UFD1 UBX2 18467557,22615397,18467557 0111,0090,0090 HT,LC UFD1 PIN3 11743162,11743162 0397,0018 HT UFD1 FMP40 10688190,10688190 0397,0018 HT UFD1 ELG1 21869594 0018 LC UFD1 SMT3 15590687,15590687 0004,0018 LC PRC1 UFD1 16179952 0007 LC RAD52 UFD1 23624404 0004 LC RPL18B UFD1 23358411 0004 LC SSA2 UFD1 16429126 0676 HT HMG2 UFD1 16179952,16179952 0004,0007 LC CDC48 UFD1 21211725,16873066,21896481,11733065,17200106,15652483,11733065,22940862,21807993,15200949,16179952,11733065,16554755,16427015,16429126,16179952,21148305,11805826,21807993,16554755,16429126,11805826,16427015,27044889,11805826 0004,0676,0004,0004,0004,0004,0018,0004,0676,0004,0004,0019,0676,0004,0676,0006,0004,0004,0096,0004,0004,0676,0096,0004,0007 LC,HT PAP1 UFD1 9236779,9236779,9236779,9236779 0019,0004,0018,0096 LC NPL4 UFD1 21211725,11733065,17200106,22940862,21070972,16179952,11733065,16554755,16429126,21070972,11805826,16554755,17289586,16429126,16179952,11598205,11805826,11805826 0004,0004,0004,0004,0007,0004,0019,0676,0676,0004,0004,0004,0096,0004,0007,0004,0676,0007 LC,HT SPT23 UFD1 17289586,16427015 0004,0004 LC RPS27A UFD1 12847084 0004 LC DOA1 UFD1 16427015,16427015,26349035,27044889 0401,0004,0004,0004 LC FZO1 UFD1 27044889 0004 LC DER1 UFD1 16179952,16179952,18407841,18407841 0004,0007,0004,0007 LC NDT80 UFD1 16554755,16554755 0676,0004 HT SSM4 UFD1 16179952,16179952,16179952 0004,0007,0006 LC MGA2 UFD1 17289586 0004 LC BNI1 UFD1 16429126 0363 HT OTU1 UFD1 16427015,16427015 0096,0004 LC BFA1 UFD1 16554755 0363 HT UFD1 UFD1 22940862,11805826,11805826 0004,0676,0007 HT UFD1 UFD2 16427015,21211725,16427015 0401,0004,0004 LC UFD1 UBX2 21211725,16873066,16179952,23793018,16179952,16179952 0004,0676,0004,0004,0007,0006 LC UFD1 VMS1 21070972 0004 LC UFD1 RQC1 23178123,23178123 0004,0007 LC UFD1 UBX5 21211725 0004 LC UFD1 HRD1 25215493,16179952,16179952 0096,0004,0007 LC UFD1 SMT3 15590687,15590687 0004,0018 LC UFD1 RQC2 23178123,23178123 0004,0007 LC UFD1 DFM1 18407841,18407841 0007,0004 LC

PPI - Mentha Protein A Protein B Gene A Gene B Score PMID P53297 P53044 PBP1 UFD1 0.309 15121841 Q12050 P53044 ELG1 UFD1 0.309 21869594 Q12221 P53044 PUF2 UFD1 0.126 26668354 Q12306 P53044 SMT3 UFD1 0.126 15590687 P53044 P0CX49 UFD1 RPL18A 0.21 23358411 P53044 P0CX50 UFD1 RPL18B 0.21 23358411 Q12532 P53044 TAE2 UFD1 0.236 23178123 Q05468 P53044 Q05468 UFD1 0.236 23178123 P53044 P38307 UFD1 DER1 0.61 18407841 P53044 P36037 UFD1 DOA1 0.309 26349035,27044889 P53044 P25694 UFD1 CDC48 0.968 16427015,15652483,16554755,16873066,27044889,21211725,11805826,16429126,11733065,21896481,25215493,21148305 P53044 P33755 UFD1 NPL4 0.97 10688190,25215493,16554755,11283351,17289586,21211725,11805826,21070972,16429126,11733065 P53044 P29468 UFD1 PAP1 0.354 9236779 P53044 P35210 UFD1 SPT23 0.21 16427015 P53044 P36094 UFD1 SPC42 0.183 17634282 P53044 P38830 UFD1 NDT80 0.236 16554755 P53044 P32526 UFD1 KAR9 0.309 18832349 P53044 P40013 UFD1 BIM1 0.309 18832349 P53044 P40460 UFD1 TID3 0.183 17634282 P53044 P47068 UFD1 BBC1 0.21 11743162 P53044 P47113 UFD1 BFA1 0.126 16554755 P53044 P48836 UFD1 VMA10 0.236 11283351 P62990 P53044 UBA52 UFD1 0.309 16004872 P53044 P41832 UFD1 BNI1 0.126 16429126 P53044 P52488 UFD1 UBA2 0.309 9236779 Q06449 P53044 PIN3 UFD1 0.332 11743162 Q06682 P53044 UBX5 UFD1 0.376 21211725 Q07807 P53044 PUF3 UFD1 0.126 26493364 Q08109 P53044 HRD1 UFD1 0.21 25215493 P54860 P53044 UFD2 UFD1 0.21 21211725 P53044 P10592 UFD1 SSA2 0.126 16429126 P53044 P06778 UFD1 RAD52 0.376 23624404 P53044 P38297 UFD1 FZO1 0.21 27044889 P53044 P35997 UFD1 RPS27A 0.21 12847084 P53044 P53044 UFD1 UFD1 0.155 11805826 Q04228 P53044 UBX2 UFD1 0.569 16873066,23793018,18467557,21211725 Q03718 P53044 NSE5 UFD1 0.126 14690591 Q08968 P53044 FMP40 UFD1 0.332 10688190 Q12743 P53044 DFM1 UFD1 0.21 18407841