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 NPL4 Ubiquinone biosynthesis monooxygenase COQ6, mitochondrial 25631044 biogrid exp RFA3 NPL4 i2d exp NPL4 PKP2 16319894 biogrid,i2d exp VMA2 NPL4 16429126 intact exp NPL4 PET130 22940862 biogrid exp NPL4 PCF11 14690591 intact exp NPL4 CUZ1 24121501,16554755 biogrid,i2d,mint,intact exp HXT4 NPL4 16429126 intact exp NPL4 RQC1 23178123 biogrid,intact exp PDC1 NPL4 11805826,16429126 biogrid,mint,intact,dip exp NPL4 YAP6 11283351 i2d,mint,intact,dip exp NPL4 SSB2 23332755 biogrid exp NPL4 BFA1 16554755 intact exp NPL4 VMS1 21070972 biogrid,i2d,intact exp NPL4 RQC2 23178123 biogrid,intact exp CMK1 NPL4 21460040 biogrid exp SBA1 NPL4 16554755 biogrid,i2d,mint,intact exp TEF1, TEF2 NPL4 16429126 intact exp NPL4 KSP1 16319894 biogrid,i2d exp NPL4 SPT23 17289586 biogrid exp NPL4 SER3 11283351 i2d,mint,intact,dip exp NPL4 UBP9 i2d exp NPL4 SER33 i2d exp NPL4 MGA2 17289586 biogrid exp NPL4 BNI1 16429126 intact exp NPL4 MIC60 21944719 biogrid exp NPL4 SHP1 i2d exp, ortho NPL4 NPL4 11805826,22940862, 23023127 biogrid,mint,intact exp, ortho, pred NPL4 UFD1 25215493,16429126,21211725,11283351,11598205,16554755,17289586,11805826,16179952,21070972,22940862,11733065,10688190, 23023127 biogrid,i2d,mint,intact,dip exp, ortho, pred CDC48 NPL4 25215493,16429126,21211725,16179953,11283351,11598205,16554755,17289586,16619026,11805826,16427015,16179952,22940862,11733065,15200949, 23023127 biogrid,i2d,mint,intact,dip exp, ortho, pred NPL4 OTU1 16427015, 23023127 biogrid exp, ortho, pred NPL4 SSM4 16873066, 23023127 biogrid exp, pred NPL4 DFM1 18407841, 23023127 biogrid,intact exp, pred NPL4 DER1 16619026,18407841, 23023127 biogrid,intact exp, pred NAB2 NPL4 19840948, 23023127 biogrid exp, pred NPL4 UFD2 16427015,21211725,18719252,11805837, 23023127 biogrid,mint,intact,dip exp, pred NPL4 UBC7 14690591, 23023127 intact exp, pred NPL4 UBX5 21211725, 23023127 biogrid exp, pred NPL4 HRD1 16619026,25215493,16179953, 23023127 biogrid,intact exp, pred NPL4 UBX2 25215493,16179952,16429126,21211725,16919153, 23023127 biogrid,intact exp, pred NPL4 HRD3 16619026,16179953, 23023127 biogrid,intact exp, pred NPL4 DOA1 16427015, 23023127 biogrid exp, pred NPL4 AOS1 ortho NPL4 GRS1 ortho SRV2 NPL4 ortho RAM1 NPL4 ortho NPL4 ADE13 ortho NPL4 FAL1 ortho NPL4 MEX67 ortho PHO85 NPL4 ortho NPL4 TRM8 ortho RAD23 NPL4 ortho UBA1 NPL4 ortho CDC19 NPL4 ortho NPL4 NCB2 ortho NPL4 UBA2 ortho RNR2 NPL4 ortho RFA2 NPL4 ortho NPL4 NUP100 23023127 pred SEC62 NPL4 23023127 pred NPL4 TIM44 23023127 pred PSE1 NPL4 23023127 pred NPL4 STS1 23023127 pred NPL4 NUP145 23023127 pred NPL4 NUP116 23023127 pred NPL4 GLE1 23023127 pred NPL4 KAP123 23023127 pred NPL4 NPL3 23023127 pred SEC61 NPL4 23023127 pred KAR2 NPL4 23023127 pred NPL4 NUP49 23023127 pred NPL4 SSS1 23023127 pred NPL4 TIM17 23023127 pred NPL4 NIC96 23023127 pred PEP1 NPL4 23023127 pred NPL4 TOM22 23023127 pred NPL4 GLE2 23023127 pred NPL4 TIM54 23023127 pred NSP1 NPL4 23023127 pred CRM1 NPL4 23023127 pred SEC63 NPL4 23023127 pred NPL4 TIM22 23023127 pred NPL4 NUP57 23023127 pred TOM40 NPL4 23023127 pred TIM23 NPL4 23023127 pred

PPI - iRefIndex UniProt A UniProt B Method PMID Interaction Type Edge type Num Participants P33755 - 11805826 - C 9 P33755 - 16179953 - C 4 P33755 - 15200949 - C 6 P33755 P40054 - 11283351 - X 2 P33755 Q03935 - 11283351 - X 2 P33755 P53044 - 10688190 - X 2 P33755 P53044 - 11283351 - X 2 P33755 P25694 - 11283351 - X 2 P33755 - 11805826 - C 4 P33755 - 11805837 - C 9 P33755 - 16179952 - C 4 P33755 - 11805826 - C 3 P0CG63 P33755 affinity chromatography technology 23749301 physical association X 2 P0CG63 P33755 biochemical 23583075 association X 2 P0CG63 P33755 affinity chromatography technology 17644757 physical association X 2 P0CG63 P33755 affinity chromatography technology 23793018 physical association X 2 P0CG63 P33755 affinity chromatography technology 12872131 physical association X 2 P40318 P33755 affinity chromatography technology 16873066 physical association X 2 P33755 P53044 affinity chromatography technology 22940862 physical association X 2 P33755 P25694 affinity chromatography technology 22940862 physical association X 2 P33755 P33755 affinity chromatography technology 22940862 physical association X 2 P33755 P25694 affinity chromatography technology 22940862 physical association X 2 P33755 P25694 affinity chromatography technology 11733065 physical association X 2 P33755 P53044 affinity chromatography technology 11733065 physical association X 2 P33755 P25694 affinity chromatography technology 11598205 physical association X 2 P33755 P53044 affinity chromatography technology 11598205 physical association X 2 P33755 Q12532 affinity chromatography technology 23178123 physical association X 2 P33755 P25694 affinity chromatography technology 15200949 physical association X 2 P33755 P25694 affinity chromatography technology 16179953 physical association X 2 P33755 P53044 pull down 17289586 direct interaction X 2 P33755 P25694 pull down 17289586 direct interaction X 2 P33755 P35210 pull down 17289586 direct interaction X 2 P33755 P25694 pull down 16427015 direct interaction X 2 P33755 P25694 pull down 16427015 direct interaction X 2 P33755 P40150 biochemical 23332755 association X 2 P33755 P25694 affinity chromatography technology 16554755 physical association X 2 P33755 P53044 affinity chromatography technology 16554755 physical association X 2 P33755 P25694 affinity chromatography technology 16429126 physical association X 2 P33755 P53044 affinity chromatography technology 16429126 physical association X 2 P33755 P25694 affinity chromatography technology 16429126 physical association X 2 P33755 P53044 affinity chromatography technology 16429126 physical association X 2 P33755 P38691 enzymatic study 16319894 direct interaction X 2 P33755 P54860 biochemical 16427015 association X 2 P33755 P54860 affinity chromatography technology 16427015 physical association X 2 P33755 P43558 pull down 16427015 direct interaction X 2 P33755 P43558 affinity chromatography technology 16427015 physical association X 2 P33755 P38307 affinity chromatography technology 16619026 physical association X 2 P33755 P25694 affinity chromatography technology 16619026 physical association X 2 P33755 P53044 affinity chromatography technology 16179952 physical association X 2 P33755 P25694 affinity chromatography technology 16179952 physical association X 2 P33755 Q04228 affinity chromatography technology 16179952 physical association X 2 P33755 P53044 affinity chromatography technology 16179952 physical association X 2 P33755 P25694 affinity chromatography technology 16179952 physical association X 2 P33755 Q04228 affinity chromatography technology 16919153 physical association X 2 P33755 P25694 affinity chromatography technology 17200106 physical association X 2 P33755 P53044 affinity chromatography technology 17200106 physical association X 2 P33755 P25694 two hybrid 11283351 direct interaction X 2 P33755 P53044 two hybrid 11283351 direct interaction X 2 P33755 P53044 two hybrid 11283351 direct interaction X 2 P33755 P54860 two hybrid 18719252 direct interaction X 2 P33755 P38307 affinity chromatography technology 18407841 physical association X 2 P33755 Q12743 affinity chromatography technology 18407841 physical association X 2 P33755 Q04311 affinity chromatography technology 21070972 physical association X 2 P33755 P53044 affinity chromatography technology 21070972 physical association X 2 P33755 P25694 affinity chromatography technology 21211725 physical association X 2 P33755 P25694 affinity chromatography technology 21211725 physical association X 2 P33755 P53044 affinity chromatography technology 21211725 physical association X 2 P33755 Q04228 affinity chromatography technology 21211725 physical association X 2 P33755 P54860 affinity chromatography technology 21211725 physical association X 2 P33755 P53044 affinity chromatography technology 21211725 physical association X 2 P33755 Q04228 affinity chromatography technology 21211725 physical association X 2 P33755 P25694 affinity chromatography technology 11805826 physical association X 2 P33755 P25694 affinity chromatography technology 11805826 physical association X 2 P33755 P06169 affinity chromatography technology 11805826 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 P54860 affinity chromatography technology 11805837 physical association X 2 P33755 P53044 two hybrid 10688190 direct interaction X 2 P53899 P33755 affinity chromatography technology 24121501 physical association X 2 P53899 P33755 affinity chromatography technology 16554755 physical association X 2 P33755 P47065 affinity chromatography technology 22940862 physical association X 2 P33755 Q05468 affinity chromatography technology 23178123 physical association X 2 P33755 Q05787 affinity chromatography technology 16179953 physical association X 2 P33755 Q08109 affinity chromatography technology 16179953 physical association X 2 P33755 P40578 pull down 17289586 direct interaction X 2 P33755 P28707 affinity chromatography technology 16554755 physical association X 2 P33755 P53170 enzymatic study 16319894 direct interaction X 2 P33755 P36037 biochemical 16427015 association X 2 P33755 P36037 affinity chromatography technology 16427015 physical association X 2 P33755 Q08109 affinity chromatography technology 16619026 physical association X 2 P33755 Q05787 affinity chromatography technology 16619026 physical association X 2 P33755 Q06682 affinity chromatography technology 21211725 physical association X 2 P33755 Q06682 affinity chromatography technology 21211725 physical association X 2 P33755 P27466 pull down 21460040 direct interaction X 2 P33755 P36112 affinity chromatography technology 21944719 physical association X 2 P33755 tandem affinity purification 11805826 - C 9 P33755 inferred by author 11805826 physical association C 14 P33755 P25694 tandem affinity purification 11805826 physical association X 2 P33755 P25694 tandem affinity purification 11805826 physical association X 2 P33755 P25694 two hybrid pooling approach 11283351 physical association X 2 P33755 Q03935 two hybrid pooling approach 11283351 physical association X 2 P33755 P40054 two hybrid pooling approach 11283351 physical association X 2 P33755 P54860 anti tag coimmunoprecipitation 11805837 physical association X 2 P33755 P06169 tandem affinity purification 11805826 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 P33755 anti tag coimmunoprecipitation 11805837 - C 9 P33755 tandem affinity purification 11805826 - C 4 P33755 tandem affinity purification 11805826 - C 3 P33755 anti tag coimmunoprecipitation 11805837 - C 12 P33755 tandem affinity purification 16429126 association C 12 P33755 tandem affinity purification 11805826 association C 4 P33755 anti tag coimmunoprecipitation 16179953 association C 4 P33755 tandem affinity purification 16429126 association C 19 P33755 anti tag coimmunoprecipitation 23178123 association C 21 P33755 molecular sieving 25215493 physical association C 3 P33755 molecular sieving 25215493 physical association C 3 P33755 anti tag coimmunoprecipitation 23178123 association C 8 P33755 anti tag coimmunoprecipitation 18407841 association C 11 P33755 tandem affinity purification 11805826 association C 10 P33755 tandem affinity purification 16429126 association C 4 P33755 pull down 25215493 association C 3 P33755 inferred by author 16554755 association C 22 P33755 P53044 two hybrid 10688190 physical association X 2 P33755 P40054 two hybrid fragment pooling approach 11283351 physical association X 2 P33755 P53044 two hybrid fragment pooling approach 11283351 physical association X 2 P33755 P25694 two hybrid fragment pooling approach 11283351 physical association X 2 P33755 Q03935 two hybrid fragment pooling approach 11283351 physical association X 2 P33755 P53044 two hybrid fragment pooling approach 11283351 physical association X 2 P33755 Q02159 two hybrid array 14690591 physical association X 2 P33755 P39081 two hybrid array 14690591 physical association X 2 P33755 P25694 tandem affinity purification 16554755 physical association X 2 P33755 P53044 tandem affinity purification 16554755 physical association X 2 P33755 P25694 tandem affinity purification 16554755 physical association X 2 P33755 P25694 tandem affinity purification 16554755 physical association X 2 P33755 P54860 two hybrid 18719252 physical association X 2 P33755 anti tag coimmunoprecipitation 18407841 association C 9 P33755 pull down 25215493 association C 4 P33755 anti tag coimmunoprecipitation 11805837 association C 9 P33755 tandem affinity purification 16429126 association C 3 P33755 anti tag coimmunoprecipitation 16919153 association C 3 P33755 tandem affinity purification 11805826 association C 5 P33755 tandem affinity purification 11805826 association C 5 P33755 anti tag coimmunoprecipitation 16179952 association C 4 P33755 molecular sieving 25215493 physical association C 4 P33755 molecular sieving 25215493 physical association C 4 P33755 molecular sieving 25215493 physical association C 3 P33755 molecular sieving 25215493 physical association C 3 P33755 tandem affinity purification 16429126 association C 6 P33755 pull down 25215493 association C 5 P33755 inferred by author 16429126 physical association C 9 P53899 P33755 tandem affinity purification 16554755 physical association X 2 P33755 P28707 tandem affinity purification 16554755 physical association X 2 P33755 mass spectrometry studies of complexes 11805826 - C 19 P33755 mass spectrometry studies of complexes 11805826 - C 19 P33755 P25694 two hybrid 11283351 - X 2 P33755 Q03935 two hybrid 11283351 - X 2 P33755 P53044 two hybrid 10688190 - X 2 P33755 P53044 two hybrid 11283351 - X 2 P33755 P14906 interaction detection method - - X 2 P33755 P40054 two hybrid 11283351 - X 2 P33755 P53044 two hybrid 11283351 - X 2 P33755 mass spectrometry studies of complexes 11805837 - C 10

PPI - HINT Gene A Gene B PMID Method Quality CDC48 NPL4 25215493,11283351,11283351,11283351 0071,0398,0399,0018 LC,HT NPL4 DOA1 16427015,16427015 0401,0004 LC NPL4 KSP1 16319894 0415 LC NPL4 PCF11 14690591 0397 LC NPL4 SER3 11283351,11283351,11283351 0018,0399,0398 HT NPL4 SSB2 23332755 0401 LC NPL4 UFD1 25215493,11733065,11283351,10688190,11733065,11283351,10688190,11283351 0071,0004,0398,0397,0019,0399,0018,0018 LC,HT NPL4 PKP2 16319894 0415 LC NPL4 UFD2 16427015,18719252,16427015 0401,0018,0004 LC,HT NPL4 UBC7 14690591 0397 LC NPL4 YAP6 11283351,11283351,11283351 0018,0399,0398 HT NPL4 UBX2 25215493 0071 LC TEF1|TEF2 NPL4 16429126 0676 HT PDC1 NPL4 11805826,16429126,11805826,11805826 0004,0676,0007,0676 HT VMA2 NPL4 16429126 0676 HT CDC48 NPL4 21211725,16619026,11733065,17200106,22940862,15200949,16179952,16179953,16554755,16427015,16429126,11805826,16179953,16554755,17289586,16429126,16179952,11598205,11805826,16427015,11805826 0004,0004,0004,0004,0004,0004,0004,0004,0676,0004,0676,0004,0007,0004,0096,0004,0007,0004,0676,0096,0007 LC,HT CMK1 NPL4 21460040 0096 LC SBA1 NPL4 16554755,16554755 0676,0004 HT HXT4 NPL4 16429126 0676 HT NAB2 NPL4 19840948 0004 LC NPL4 NPL4 22940862,16179952,11805826,11805826 0004,0004,0676,0007 HT,LC NPL4 SPT23 17289586,17289586 0004,0096 LC NPL4 DOA1 16427015,26349035,16427015 0401,0004,0004 LC NPL4 MIC60 21944719 0004 LC NPL4 DER1 18407841,18407841,16619026 0007,0004,0004 LC NPL4 SSB2 23332755 0401 LC NPL4 SSM4 16873066 0004 LC NPL4 MGA2 17289586,17289586 0004,0096 LC NPL4 BNI1 16429126 0363 HT NPL4 OTU1 16427015,16427015 0096,0004 LC NPL4 PET130 22940862 0004 HT NPL4 BFA1 16554755 0363 HT 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 NPL4 COQ6 25631044 0004 LC NPL4 CUZ1 16554755,16554755,24121501 0004,0676,0004 HT,LC NPL4 UFD2 16427015,11805837,21211725,16427015,11805837 0401,0004,0004,0004,0007 LC,HT NPL4 UBX2 21211725,16429126,16179952,16919153,16179952,16919153 0004,0676,0007,0004,0004,0007 LC,HT NPL4 VMS1 21070972,21070972 0004,0007 LC NPL4 RQC1 23178123,23178123 0004,0007 LC NPL4 HRD3 16179953,16179953,16619026 0004,0007,0004 LC NPL4 UBX5 21211725 0004 LC NPL4 HRD1 25215493,16179953,16619026,16179953 0096,0004,0004,0007 LC NPL4 RQC2 23178123,23178123 0004,0007 LC NPL4 DFM1 18407841,18407841 0007,0004 LC

PPI - Mentha Protein A Protein B Gene A Gene B Score PMID P53170 P33755 PKP2 NPL4 0.183 16319894 P53318 P33755 COQ6 NPL4 0.21 25631044 P33755 P06169 NPL4 PDC1 0.332 11805826,16429126 Q12532 P33755 TAE2 NPL4 0.236 23178123 Q12743 P33755 DFM1 NPL4 0.376 18407841 Q04228 P33755 UBX2 NPL4 0.569 16429126,25215493,21211725 Q04311 P33755 VMS1 NPL4 0.376 21070972 Q05468 P33755 Q05468 NPL4 0.236 23178123 P33755 P28707 NPL4 SBA1 0.236 16554755 P33755 P25694 NPL4 CDC48 0.964 16427015,16429126,25215493,16554755,11283351,17289586,21211725,11805826,16179953 P53899 P33755 P53899 NPL4 0.309 16554755,24121501 P38307 P33755 DER1 NPL4 0.376 18407841 P53044 P33755 UFD1 NPL4 0.97 10688190,25215493,16554755,11283351,17289586,21211725,11805826,21070972,16429126,11733065 P33755 P32467 NPL4 HXT4 0.126 16429126 P38691 P33755 KSP1 NPL4 0.183 16319894 P33755 P32505 NPL4 NAB2 0.126 19840948 P33755 P27466 NPL4 CMK1 0.183 21460040 P36112 P33755 FCJ1 NPL4 0.126 21944719 P33755 P02994 NPL4 TEF2 0.126 16429126 P33755 P16140 NPL4 VMA2 0.126 16429126 P33755 P33755 NPL4 NPL4 0.155 11805826 P35210 P33755 SPT23 NPL4 0.309 17289586 P39081 P33755 PCF11 NPL4 0.126 14690591 P40054 P33755 SER3 NPL4 0.236 11283351 P40578 P33755 MGA2 NPL4 0.309 17289586 P54860 P33755 UFD2 NPL4 0.648 11805837,18719252,21211725 Q02159 P33755 UBC7 NPL4 0.126 14690591 Q05787 P33755 HRD3 NPL4 0.21 16179953 Q06682 P33755 UBX5 NPL4 0.376 21211725 Q08109 P33755 HRD1 NPL4 0.376 25215493,16179953 P36037 P33755 DOA1 NPL4 0.126 26349035 P47113 P33755 BFA1 NPL4 0.126 16554755 P41832 P33755 BNI1 NPL4 0.126 16429126 Q03935 P33755 YAP6 NPL4 0.21 11283351