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 VPS15 HSP78 19536198 intact exp VPS15 SEC21 23904270 biogrid exp VPS15 COY1 23904270 biogrid exp VPS15 BET1 23904270 biogrid exp VPS15 UBC7 14690591 intact exp VPS15 SEC17 23904270 biogrid exp VPS15 PIL1 23904270 biogrid exp VPS15 AIM3 16554755 intact exp VPS15 DNF1 23904270 biogrid exp VPS15 APM3 i2d exp VPS15 SVP26 23904270 biogrid exp UBI4 VPS15 21070969 biogrid exp ACO1 VPS15 i2d exp VPS15 EMP47 23904270 biogrid exp VPS15 YHB1 16429126 intact exp VPS15 SSP120 23904270 biogrid exp VPS15 NEO1 23904270 biogrid exp VPS15 SFT2 23904270 biogrid exp VPS15 CDC48 23904270 biogrid exp HTB2 VPS15 i2d exp VPS15 ATG38 24165940 biogrid exp SEC4 VPS15 23904270 biogrid exp VPS15 GOS1 23904270 biogrid exp VPS15 FKS1 23904270 biogrid exp PMR1 VPS15 23904270 biogrid exp SSB1 VPS15 19536198 intact exp VPS15 HSP42 19536198 intact exp VPS15 DID2 23904270 biogrid exp VPS15 TVP38 23904270 biogrid exp VPS15 SFT1 23904270 biogrid exp VPS15 SSO1 23904270 biogrid exp VPS15 YPT7 23904270 biogrid exp VPS15 VPS15 23904270 biogrid exp VPS15 STV1 23904270 biogrid exp VPS15 PEP12 23904270 biogrid exp VPS15 SSE1 19536198 intact exp VPS15 SNF7 23904270 biogrid exp SEC22 VPS15 23904270 biogrid exp VPS15 AKR1 23904270 biogrid exp VPS15 DID4 23904270 biogrid exp VPS15 ERV25 23904270 biogrid exp VPS15 YOP1 23904270 biogrid exp VPS15 YIP3 23904270 biogrid exp VPS15 DAK2 18467557 biogrid,i2d,mint,intact exp SEC23 VPS15 23904270 biogrid exp VPS15 VPS30 11157979,16429126,23904270,16421251, 23023127 biogrid,intact exp, ortho, pred VPS15 VPS34 8387919,20489023,23904270,11689570,24165940, 23023127 biogrid,i2d,mint,intact,dip exp, ortho, pred VPS15 YPT52 23904270, 23023127 biogrid exp, pred VPS15 YPT31 23904270, 23023127 biogrid exp, pred VPS15 YCK3 23904270, 23023127 biogrid exp, pred YPT1 VPS15 23904270, 23023127 biogrid exp, pred VPS15 ATG14 11157979,19445518,23904270,24165940, 23023127 biogrid,intact exp, pred VPS15 PTC3 11805826,16429126, 23023127 biogrid,mint,intact,dip exp, pred VPS15 VPS21 23904270, 23023127 biogrid exp, pred GPA1 VPS15 19445518,16839886, 23023127 biogrid,intact exp, pred VPS15 VTI1 23904270, 23023127 biogrid exp, pred VPS1 VPS15 23904270, 23023127 biogrid exp, pred VPS15 PEP1 23904270, 23023127 biogrid exp, pred VPS15 EMP24 23904270, 23023127 biogrid exp, pred VPS15 VPS38 11157979,16429126,23904270, 23023127 biogrid,intact exp, pred VPS15 RVS167 16554755, 23023127 biogrid,i2d,mint,intact exp, pred VPS15 HRR25 ortho VPS15 PPT1 ortho VPS15 MEX67 ortho VPS15 CRM1 ortho VPS15 BIM1 ortho VPS15 ARL1 23023127 pred VPS15 VPS27 23023127 pred VPS15 YPT6 23023127 pred VPS15 PEX7 23023127 pred VPS15 ATG3 23023127 pred VPS15 SEC27 23023127 pred VPS15 VPS29 23023127 pred ERD2 VPS15 23023127 pred SLY1 VPS15 23023127 pred VPS15 VPS5 23023127 pred ARF2 VPS15 23023127 pred VPS15 LST8 23023127 pred VPS15 UBI4 23023127 pred VPS15 VPS4 23023127 pred VPS15 ATG4 23023127 pred VPS15 VPS35 23023127 pred VPS15 VPS3 23023127 pred VPS15 TLG2 23023127 pred VPS15 PEP3 23023127 pred VPS15 ATG8 23023127 pred VPS15 SNX3 23023127 pred VPS33 VPS15 23023127 pred VPS15 ATG1 23023127 pred VPS15 ATG20 23023127 pred VPS15 RER1 23023127 pred

PPI - iRefIndex UniProt A UniProt B Method PMID Interaction Type Edge type Num Participants P38270 P22219 affinity chromatography technology 11157979 physical association X 2 P38270 P22219 affinity chromatography technology 19445518 physical association X 2 P22543 P22219 affinity chromatography technology 8387919 physical association X 2 P22543 P22219 biochemical 8387919 colocalization X 2 P22543 P22219 two hybrid 11689570 direct interaction X 2 P22543 P22219 affinity chromatography technology 11689570 physical association X 2 P22543 P22219 affinity chromatography technology 20489023 physical association X 2 Q02948 P22219 affinity chromatography technology 16429126 physical association X 2 Q02948 P22219 affinity chromatography technology 16421251 physical association X 2 Q02948 P22219 affinity chromatography technology 17200106 physical association X 2 P22219 P43550 protein complementation assay 18467557 direct interaction X 2 P08539 P22219 affinity chromatography technology 16839886 physical association X 2 P08539 P22219 pull down 16839886 direct interaction X 2 P08539 P22219 affinity chromatography technology 19445518 physical association X 2 P0CG63 P22219 affinity chromatography technology 23749301 physical association X 2 P0CG63 P22219 affinity chromatography technology 23793018 physical association X 2 P0CG63 P22219 pull down 21070969 direct interaction X 2 P22219 P39743 affinity chromatography technology 16554755 physical association X 2 P22219 P34221 affinity chromatography technology 16429126 physical association X 2 P22219 P34221 affinity chromatography technology 11805826 physical association X 2 Q05919 P22219 affinity chromatography technology 11157979 physical association X 2 Q05919 P22219 affinity chromatography technology 16429126 physical association X 2 Q05919 P22219 affinity chromatography technology 17200106 physical association X 2 P22219 tandem affinity purification 11805826 physical association C 8 P22219 inferred by author 11805826 physical association C 8 P22543 P22219 cross-linking study 8387919 direct interaction X 2 P22543 P22219 coimmunoprecipitation 8387919 direct interaction X 2 P22219 P34221 tandem affinity purification 11805826 physical association X 2 P22219 tandem affinity purification 20489023 association C 3 P22219 anti bait coimmunoprecipitation 11157979 association C 4 P22219 anti bait coimmunoprecipitation 11157979 association C 4 P22219 inferred by author 16429126 physical association C 4 P22219 inferred by author 16554755 association C 17 P22219 tandem affinity purification 16429126 association C 6 P32589 P22219 tandem affinity purification 19536198 association X 2 P22543 P22219 tandem affinity purification 20489023 association X 2 P22219 P43550 dihydrofolate reductase reconstruction 18467557 physical association X 2 P22219 P33416 tandem affinity purification 19536198 association X 2 P22219 Q12329 tandem affinity purification 19536198 association X 2 P08539 P22219 tandem affinity purification 16839886 physical association X 2 P08539 P22219 pull down 16839886 physical association X 2 P22219 tandem affinity purification 11805826 association C 9 P22219 inferred by author 16429126 physical association C 9 P22219 tandem affinity purification 16429126 association C 17 P22219 anti tag coimmunoprecipitation 11157979 association C 5 P22219 anti bait coimmunoprecipitation 11157979 association C 4 P22219 tandem affinity purification 16429126 association C 8 P11484 P22219 tandem affinity purification 19536198 association X 2 Q02159 P22219 two hybrid array 14690591 physical association X 2 P22219 P39743 tandem affinity purification 16554755 physical association X 2 P22543 P22219 protein cross-linking with a bifunctional reagent 11157979,8387919 - X 2 P22219 P22219 confirmational text mining - - Y 1 P22219 mass spectrometry studies of complexes 11805826 - C 9 P38153 P22219 interaction detection method 9412470 - X 2

PPI - HINT Gene A Gene B PMID Method Quality VPS15 VPS34 27630019,8387919,11689570,8387919,11689570,26450213,8387919,8387919,8387919,11157979 0114,0031,0018,0019,0004,0114,0004,0401,0030,0031 LC VPS15 DAK2 18467557,18467557 0111,0090 HT VPS15 UBC7 14690591 0397 LC VPS15 VPS38 26450213 0114 LC YPT1 VPS15 23904270 0004 LC SEC4 VPS15 23904270 0004 LC GPA1 VPS15 16839886,19445518,16839886,16839886 0676,0004,0004,0096 LC UBI4 VPS15 21070969,21070969 0004,0096 LC SSB1 VPS15 19536198 0676 HT PMR1 VPS15 23904270 0004 LC SEC23 VPS15 23904270 0004 LC VPS1 VPS15 23904270 0004 LC SEC22 VPS15 23904270 0004 LC VPS15 VPS15 23904270 0004 LC VPS15 VPS34 20489023,23904270,20489023,8387919,11689570,8387919,11689570,20489023,8387919,8387919,8387919,24165940 0676,0004,0007,0031,0018,0019,0004,0004,0004,0401,0030,0004 HT,LC VPS15 BET1 23904270 0004 LC VPS15 CDC48 23904270 0004 LC VPS15 SEC21 23904270 0004 LC VPS15 PEP1 23904270 0004 LC VPS15 SSE1 19536198 0676 HT VPS15 DNF1 23904270 0004 LC VPS15 EMP24 23904270 0004 LC VPS15 PEP12 23904270 0004 LC VPS15 SSO1 23904270 0004 LC VPS15 YPT7 23904270 0004 LC VPS15 HSP78 19536198 0676 HT VPS15 SAS3 23904270 0004 LC VPS15 TOD6 11805826,16429126,11805826,16429126,11805826 0004,0004,0007,0676,0676 HT VPS15 COY1 23904270 0004 LC VPS15 VPS21 23904270 0004 LC VPS15 YPT52 23904270 0004 LC VPS15 DID4 23904270 0004 LC VPS15 TVP38 23904270 0004 LC VPS15 STV1 23904270 0004 LC VPS15 SFT2 23904270 0004 LC VPS15 AIM3 16554755 0363 HT VPS15 ATG14 19445518,11157979,23904270,24165940,11157979 0004,0006,0004,0004,0004 LC VPS15 YPT31 23904270 0004 LC VPS15 FKS1 23904270 0004 LC VPS15 GOS1 23904270 0004 LC VPS15 SVP26 23904270 0004 LC VPS15 AKR1 23904270 0004 LC VPS15 YHB1 16429126 0363 HT VPS15 RVS167 16554755,16554755 0676,0004 HT VPS15 SNF7 23904270 0004 LC VPS15 SSP120 23904270 0004 LC VPS15 YCK3 23904270 0004 LC VPS15 NEO1 23904270 0004 LC VPS15 EMP47 23904270 0004 LC VPS15 SFT1 23904270 0004 LC VPS15 PIL1 23904270 0004 LC VPS15 YIP3 23904270 0004 LC VPS15 ERV25 23904270 0004 LC VPS15 DID2 23904270 0004 LC VPS15 VPS30 23904270,16429126,11157979,11157979,17200106,16429126,16429126,16421251 0004,0676,0007,0006,0004,0363,0004,0004 LC,HT VPS15 VTI1 23904270 0004 LC VPS15 ATG38 24165940,24165940 0096,0004 LC VPS15 VPS38 23904270,16429126,11157979,17200106,16429126,11157979 0004,0676,0006,0004,0004,0004 LC,HT VPS15 HSP42 19536198 0676 HT VPS15 YOP1 23904270 0004 LC

PPI - Mentha Protein A Protein B Gene A Gene B Score PMID P22219 P0CG63 VPS15 UBI4 0.309 21070969 P22219 P11484 VPS15 SSB1 0.126 19536198 P22543 P22219 VPS34 VPS15 0.872 11689570,8387919,23904270,20489023,24165940 P22219 P08539 VPS15 GPA1 0.731 19445518,16839886 P38270 P22219 ATG14 VPS15 0.702 11157979,24165940,23904270,19445518 P43550 P22219 DAK2 VPS15 0.286 18467557 Q05789 P22219 Q05789 VPS15 0.659 24165940 P38266 P22219 AIM3 VPS15 0.126 16554755 P32589 P22219 SSE1 VPS15 0.126 19536198 P39676 P22219 YHB1 VPS15 0.126 16429126 P39743 P22219 RVS167 VPS15 0.236 16554755 P33416 P22219 HSP78 VPS15 0.126 19536198 P34221 P22219 PTC3 VPS15 0.354 11805826,16429126 P22219 P01123 VPS15 YPT1 0.126 23904270 P22219 P07560 VPS15 SEC4 0.126 23904270 P22219 P13586 VPS15 PMR1 0.126 23904270 P22219 P15303 VPS15 SEC23 0.126 23904270 P22219 P21576 VPS15 VPS1 0.126 23904270 P22219 P22214 VPS15 SEC22 0.126 23904270 P22219 P22219 VPS15 VPS15 0.155 23904270 P22804 P22219 BET1 VPS15 0.126 23904270 P25694 P22219 CDC48 VPS15 0.126 23904270 P32074 P22219 SEC21 VPS15 0.126 23904270 P32319 P22219 PEP1 VPS15 0.126 23904270 P32602 P22219 SEC17 VPS15 0.126 23904270 P32660 P22219 DNF1 VPS15 0.126 23904270 P32803 P22219 EMP24 VPS15 0.126 23904270 P32854 P22219 PEP12 VPS15 0.126 23904270 P32867 P22219 SSO1 VPS15 0.126 23904270 P32939 P22219 YPT7 VPS15 0.126 23904270 P34237 P22219 COY1 VPS15 0.126 23904270 P36017 P22219 VPS21 VPS15 0.126 23904270 P36018 P22219 YPT52 VPS15 0.126 23904270 P36108 P22219 DID4 VPS15 0.126 23904270 P36164 P22219 TVP38 VPS15 0.126 23904270 P37296 P22219 STV1 VPS15 0.126 23904270 P38166 P22219 SFT2 VPS15 0.126 23904270 P38555 P22219 YPT31 VPS15 0.126 23904270 P38631 P22219 FKS1 VPS15 0.126 23904270 P38736 P22219 GOS1 VPS15 0.126 23904270 P38869 P22219 SVP26 VPS15 0.126 23904270 P39010 P22219 AKR1 VPS15 0.126 23904270 P39929 P22219 SNF7 VPS15 0.126 23904270 P39931 P22219 SSP120 VPS15 0.126 23904270 P39962 P22219 YCK3 VPS15 0.126 23904270 P40527 P22219 NEO1 VPS15 0.126 23904270 P43555 P22219 EMP47 VPS15 0.126 23904270 P43682 P22219 SFT1 VPS15 0.126 23904270 P53252 P22219 PIL1 VPS15 0.126 23904270 P53633 P22219 YIP3 VPS15 0.126 23904270 P54837 P22219 ERV25 VPS15 0.126 23904270 P69771 P22219 DID2 VPS15 0.126 23904270 Q02159 P22219 UBC7 VPS15 0.126 14690591 Q02948 P22219 VPS30 VPS15 0.539 16421251,16429126,23904270 Q04338 P22219 VTI1 VPS15 0.126 23904270 Q05919 P22219 VPS38 VPS15 0.396 11157979,16429126,23904270 Q12329 P22219 HSP42 VPS15 0.126 19536198 Q12402 P22219 YOP1 VPS15 0.126 23904270