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 ATG18 MCD1 i2d exp VPS35 ATG18 23904270 biogrid exp VPS29 ATG18 23904270 biogrid exp FAB1 ATG18 11536337,19037259 biogrid,intact exp SSB2 ATG18 23332755,19536198 biogrid,intact exp ATG18 DID2 23904270 biogrid exp ATG18 BIO3 11536337 biogrid,dip exp SFT2 ATG18 23904270 biogrid exp RTG3 ATG18 11536337 biogrid,dip exp ATG18 RTC4 i2d exp ATG18 CDC55 11805837 biogrid,intact,dip exp TEF1, TEF2 ATG18 16429126 intact exp FIG4 ATG18 19037259 intact exp SSA2 ATG18 16429126,19536198 intact exp YPT7 ATG18 23904270 biogrid exp MAS2 ATG18 i2d exp SWE1 ATG18 16319894 biogrid,i2d exp SSA4 ATG18 11805837 dip exp ATG18 SAP155 16554755,11805837 biogrid,i2d,mint,intact,dip exp VPS1 ATG18 23904270 biogrid exp GAL7 ATG18 11805837 dip exp ATG18 FAS1 domain-containing protein YLR001C i2d exp AIM46 ATG18 11805837 dip exp ATG18 TOS3 16319894 biogrid,i2d exp ATG18 UBC7 14690591 intact exp SEC4 ATG18 23904270 biogrid exp SSA1 ATG18 19536198 intact exp RAD53 ATG18 doi:10.1038/emboj.2012.28,22333915 mint,intact exp VAC17 ATG18 11536337,17699591,18467557 biogrid,mint,intact,dip exp HSP82 ATG18 19536198 intact exp SEC23 ATG18 23904270 biogrid exp PEP8 ATG18 23904270 biogrid exp UBI4 ATG18 21070969 biogrid exp LYS14 ATG18 11283351 i2d,mint,intact,dip exp RPP0 ATG18 16429126 intact exp ATG18 UTP13 11805837 biogrid,intact,dip exp TDH1 ATG18 11805837 dip exp GVP36 ATG18 23904270 biogrid exp SAC6 ATG18 23904270 biogrid exp ATG18 THI21 11805837 biogrid,mint,intact,dip exp ATG18 VAC7 19037259 intact exp ATG18 HIR3 11536337 biogrid,dip exp LEU2 ATG18 11805837 dip exp RPS3 ATG18 16429126 intact exp SSO1 ATG18 23904270 biogrid exp SSB1 ATG18 19536198 intact exp ATG18 GIS3 11536337 biogrid,dip exp CDC48 ATG18 23904270 biogrid exp RRP1 ATG18 i2d exp INO1 ATG18 11805837 dip exp SEC26 ATG18 23904270 biogrid exp SBE22 ATG18 11536337 biogrid,dip exp ATG18 PTR3 11536337 biogrid exp SEC21 ATG18 23904270 biogrid exp ATG18 BNA1 11536337 biogrid exp ATG18 ATG18 11805826, 23023127 mint,intact exp, ortho, pred PHO85 ATG18 16319894, 23023127 biogrid,i2d exp, pred AKL1 ATG18 16319894, 23023127 biogrid,i2d exp, pred YCK1 ATG18 16319894, 23023127 biogrid exp, pred ATG18 ATG2 21887408,16429126,23230146,23904270,18586673,22728243,16554755,11805837,22851171,11805826,17295840, 23023127 biogrid,i2d,mint,intact,dip exp, pred ATG18 ATG1 16319894, 23023127 biogrid,i2d exp, pred ATG18 ATG9 24440502,18829864,14723849, 23023127 biogrid,intact exp, pred ATG18 VAC14 19037259,18467557, 23023127 biogrid,i2d,mint,intact exp, pred SIT4 ATG18 11805837, 23023127 biogrid,mint,intact,dip exp, pred ADH1 ATG18 11805826,16429126,21036361, 23023127 biogrid,mint,intact,dip exp, pred TRM5 ATG18 16554755, 23023127 biogrid,i2d,mint,intact exp, pred ATG18 LSB3 19841731, 23023127 biogrid,mint,intact exp, pred RAD4 ATG18 11536337, 23023127 biogrid,dip exp, pred ATG18 NTE1 11536337, 23023127 biogrid,dip exp, pred ATG18 PEX13 19841731, 23023127 biogrid,mint,intact exp, pred DPH2 ATG18 ortho TIF34 ATG18 ortho SIS1 ATG18 ortho GCN1 ATG18 ortho DPH1 ATG18 ortho STI1 ATG18 ortho ATG18 PPT1 ortho PFK1 ATG18 ortho

PPI - iRefIndex UniProt A UniProt B Method PMID Interaction Type Edge type Num Participants Q05946 P43601 - 11805837 - X 2 P43601 - 11805837 - C 4 P43601 - 11805826 - C 3 P43601 - 11805837 - C 4 P43601 Q12418 two hybrid 11536337 direct interaction X 2 P43601 P47171 two hybrid 11536337 direct interaction X 2 P43601 P43637 enzymatic study 16319894 direct interaction X 2 P43601 P23291 enzymatic study 16319894 direct interaction X 2 P43601 P43603 two hybrid 19841731 direct interaction X 2 P43601 P80667 two hybrid 19841731 direct interaction X 2 P43601 P00330 affinity chromatography technology 11805826 physical association X 2 P43601 Q00362 affinity chromatography technology 11805837 physical association X 2 P38165 P43601 two hybrid 11536337 direct interaction X 2 P53104 P43601 enzymatic study 16319894 direct interaction X 2 P38814 P43601 two hybrid 11536337 direct interaction X 2 P43606 P43601 two hybrid 11536337 direct interaction X 2 Q05946 P43601 affinity chromatography technology 11805837 physical association X 2 P43612 P43601 affinity chromatography technology 16554755 physical association X 2 P43612 P43601 affinity chromatography technology 11805837 physical association X 2 P34756 P43601 two hybrid 11536337 direct interaction X 2 P50277 P43601 two hybrid 11536337 direct interaction X 2 P38080 P43601 enzymatic study 16319894 direct interaction X 2 P43601 P25591 two hybrid 11536337 direct interaction X 2 P43601 P14736 two hybrid 11536337 direct interaction X 2 P43601 P38793 affinity chromatography technology 16554755 physical association X 2 P43601 P32944 enzymatic study 16319894 direct interaction X 2 P43601 P25591 two hybrid 17699591 direct interaction X 2 P43601 P25591 affinity chromatography technology 17699591 physical association X 2 P43601 P25591 protein complementation assay 18467557 direct interaction X 2 P43601 Q06708 protein complementation assay 18467557 direct interaction X 2 P43601 Q06708 two hybrid 19037259 direct interaction X 2 P43601 P17157 enzymatic study 16319894 direct interaction X 2 Q04958 P43601 two hybrid 11536337 direct interaction X 2 P0CG63 P43601 biochemical 23583075 association X 2 P0CG63 P43601 affinity chromatography technology 23793018 physical association X 2 P0CG63 P43601 pull down 21070969 direct interaction X 2 Q2TAZ0 P43601 two hybrid 21887408 direct interaction X 2 Q2TAZ0 P43601 imaging technique 21887408 colocalization X 2 Q08975 P43601 affinity chromatography technology 11805837 physical association X 2 P20604 P43601 affinity chromatography technology 11805837 physical association X 2 Q12142 P43601 affinity chromatography technology 14723849 physical association X 2 Q12142 P43601 two hybrid 18829864 direct interaction X 2 P47096 P43601 two hybrid 11536337 direct interaction X 2 P53855 P43601 imaging technique 22728243 colocalization X 2 P53855 P43601 two hybrid 21887408 direct interaction X 2 P53855 P43601 imaging technique 21887408 colocalization X 2 P53855 P43601 affinity chromatography technology 22851171 physical association X 2 P53855 P43601 affinity chromatography technology 16554755 physical association X 2 P53855 P43601 affinity chromatography technology 17200106 physical association X 2 P53855 P43601 affinity chromatography technology 18586673 physical association X 2 P53855 P43601 affinity chromatography technology 17295840 physical association X 2 P53855 P43601 affinity chromatography technology 11805826 physical association X 2 P53855 P43601 affinity chromatography technology 11805837 physical association X 2 P40150 P43601 biochemical 23332755 association X 2 P43601 anti tag coimmunoprecipitation 11805837 - C 7 P00360 P43601 anti tag coimmunoprecipitation 11805837 physical association X 2 P43601 Q12418 two hybrid 11536337 physical association X 2 P43601 P47171 two hybrid 11536337 physical association X 2 P43601 Q00362 anti tag coimmunoprecipitation 11805837 physical association X 2 P43601 P00330 tandem affinity purification 11805826 physical association X 2 P11986 P43601 anti tag coimmunoprecipitation 11805837 physical association X 2 P38165 P43601 two hybrid 11536337 physical association X 2 P38814 P43601 two hybrid 11536337 physical association X 2 P04173 P43601 anti tag coimmunoprecipitation 11805837 physical association X 2 Q05946 P43601 anti tag coimmunoprecipitation 11805837 physical association X 2 P38885 P43601 anti tag coimmunoprecipitation 11805837 physical association X 2 P50277 P43601 two hybrid 11536337 physical association X 2 P43601 tandem affinity purification 11805826 physical association C 3 P43601 inferred by author 11805826 physical association C 3 P43601 anti tag coimmunoprecipitation 11805837 - C 13 P08431 P43601 anti tag coimmunoprecipitation 11805837 physical association X 2 P43601 P25591 two hybrid 11536337 physical association X 2 P43601 P14736 two hybrid 11536337 physical association X 2 P43601 anti tag coimmunoprecipitation 11805837 physical association X 2 Q04958 P43601 two hybrid 11536337 physical association X 2 Q08975 P43601 anti tag coimmunoprecipitation 11805837 physical association X 2 P20604 P43601 anti tag coimmunoprecipitation 11805837 physical association X 2 P53855 P43601 tandem affinity purification 11805826 physical association X 2 P53855 P43601 anti tag coimmunoprecipitation 11805837 physical association X 2 P22202 P43601 anti tag coimmunoprecipitation 11805837 physical association X 2 P40971 P43601 two hybrid pooling approach 11283351 physical association X 2 P43601 anti tag coimmunoprecipitation 11805837 association C 4 P43601 tandem affinity purification 16429126 association C 7 P22216 P43601 protein kinase assay 22333915 phosphorylation reaction X 2 P43601 P43603 two hybrid array 19841731 physical association X 2 P43601 P80667 two hybrid array 19841731 physical association X 2 Q02159 P43601 two hybrid array 14690591 physical association X 2 Q05946 P43601 anti tag coimmunoprecipitation 11805837 physical association X 2 P43612 P43601 tandem affinity purification 16554755 physical association X 2 P43612 P43601 tandem affinity purification 16554755 physical association X 2 P43612 P43601 tandem affinity purification 16554755 physical association X 2 P43612 P43601 tandem affinity purification 16554755 physical association X 2 P10591 P43601 tandem affinity purification 19536198 association X 2 P43601 tandem affinity purification 11805826 association C 4 P43601 tandem affinity purification 11805826 association C 4 P43601 anti tag coimmunoprecipitation 11805837 association C 4 P43601 cosedimentation through density gradient 19037259 colocalization C 5 P10592 P43601 tandem affinity purification 19536198 association X 2 P11484 P43601 tandem affinity purification 19536198 association X 2 P43601 P38793 inferred by author 16554755 association X 2 P43601 P38793 tandem affinity purification 16554755 physical association X 2 P43601 P38793 tandem affinity purification 16554755 physical association X 2 P43601 P38793 tandem affinity purification 16554755 physical association X 2 P43601 P25591 dihydrofolate reductase reconstruction 18467557 physical association X 2 P43601 Q06708 dihydrofolate reductase reconstruction 18467557 physical association X 2 P43601 Q06708 two hybrid 19037259 physical association X 2 P43601 Q06708 two hybrid 19037259 physical association X 2 P43601 Q06708 fluorescence microscopy 19037259 colocalization X 2 P02829 P43601 tandem affinity purification 19536198 association X 2 Q12142 P43601 affinity chromatography technology 14723849 physical association X 2 P53855 P43601 tandem affinity purification 16554755 physical association X 2 P53855 P43601 tandem affinity purification 16554755 physical association X 2 P53855 P43601 tandem affinity purification 16554755 physical association X 2 P53855 P43601 tandem affinity purification 16554755 physical association X 2 P53855 P43601 tandem affinity purification 16554755 physical association X 2 P53855 P43601 tandem affinity purification 16554755 physical association X 2 P40150 P43601 tandem affinity purification 19536198 association X 2 P40971 P43601 two hybrid fragment pooling approach 11283351 physical association X 2 P43601 mass spectrometry studies of complexes 11805837 - C 8 P43601 mass spectrometry studies of complexes 11805837 - C 8 P43601 mass spectrometry studies of complexes 11805826 - C 4 P43601 mass spectrometry studies of complexes 11805826 - C 4 P40971 P43601 two hybrid 11283351 - X 2

PPI - HINT Gene A Gene B PMID Method Quality ADH1 ATG18 21036361 0401 LC RAD4 ATG18 11536337 0018 LC PHO85 ATG18 16319894 0415 LC RAD53 ATG18 22333915 0424 LC YCK1 ATG18 16319894 0415 LC VAC17 ATG18 11536337,17699591,18467557,18467557,17699591 0018,0004,0111,0090,0018 LC,HT SWE1 ATG18 16319894 0415 LC FAB1 ATG18 11536337,19037259 0018,0029 LC AKL1 ATG18 16319894 0415 LC RTG3 ATG18 11536337 0018 LC SBE22 ATG18 11536337 0018 LC SSB2 ATG18 23332755 0401 LC LYS14 ATG18 11283351,11283351,11283351 0018,0399,0398 HT FIG4 ATG18 19037259 0029 LC ATG18 LSB3 19841731,19841731 0397,0018 HT ATG18 PTR3 11536337 0018 LC ATG18 TOS3 16319894 0415 LC ATG18 BNA1 11536337 0018 LC ATG18 HIR3 11536337 0018 LC ATG18 BIO3 11536337 0018 LC ATG18 ATG1 16319894 0415 LC ATG18 ATG2 23230146,23230146,23230146,21887408,21887408 0809,0018,0004,0428,0018 LC ATG18 VAC7 19037259 0029 LC ATG18 PEX13 19841731,19841731 0397,0018 HT ATG18 UBC7 14690591 0397 LC ATG18 NTE1 11536337 0018 LC ATG18 VAC14 19037259,19037259,18467557,18467557,19037259 0029,0018,0111,0090,0416 LC,HT ATG18 ATG9 18829864 0018 LC ATG18 GIS3 11536337 0018 LC ADH1 ATG18 11805826,11805826,16429126,11805826,21036361 0676,0007,0676,0004,0401 HT,LC TDH1 ATG18 11805837 0007 HT HSP82 ATG18 19536198 0676 HT TEF1|TEF2 ATG18 16429126 0676 HT LEU2 ATG18 11805837 0007 HT RPP0 ATG18 16429126 0676 HT RPS3 ATG18 16429126 0676 HT SEC4 ATG18 23904270 0004 LC GAL7 ATG18 11805837 0007 HT UBI4 ATG18 21070969,21070969 0004,0096 LC SSA1 ATG18 19536198 0676 HT SSA2 ATG18 19536198,16429126 0676,0676 HT SSB1 ATG18 19536198 0676 HT INO1 ATG18 11805837 0007 HT SEC23 ATG18 23904270 0004 LC SIT4 ATG18 11805837,11805837 0004,0007 HT VPS1 ATG18 23904270 0004 LC SSA4 ATG18 11805837 0007 HT VAC17 ATG18 17699591,17699591 0004,0018 LC CDC48 ATG18 23904270 0004 LC SEC21 ATG18 23904270 0004 LC SAC6 ATG18 23904270 0004 LC SSO1 ATG18 23904270 0004 LC YPT7 ATG18 23904270 0004 LC VPS35 ATG18 23904270 0004 LC SFT2 ATG18 23904270 0004 LC VPS29 ATG18 23904270 0004 LC TRM5 ATG18 16554755,16554755,16554755 0363,0676,0004 HT AIM46 ATG18 11805837 0007 HT SSB2 ATG18 19536198,23332755 0676,0401 HT,LC PEP8 ATG18 23904270 0004 LC GVP36 ATG18 23904270 0004 LC SEC26 ATG18 23904270 0004 LC ATG18 ATG18 11805826,11805826 0676,0007 HT ATG18 SAP155 11805837,16554755,11805837,16554755 0004,0676,0007,0004 HT ATG18 ATG2 11805837,22728243,16554755,23904270,18586673,22851171,16429126,23230146,11805826,11805837,11805826,23230146,23230146,16554755,17200106,11805826,17295840,21887408,21887408 0004,0428,0676,0004,0004,0004,0676,0809,0004,0007,0676,0018,0004,0004,0004,0007,0004,0428,0018 HT,LC ATG18 DID2 23904270 0004 LC ATG18 CDC55 11805837,11805837 0004,0007 HT ATG18 UTP13 11805837,11805837 0004,0007 HT ATG18 THI21 11805837,11805837 0004,0007 HT ATG18 ATG9 24440502,14723849 0004,0004 LC

PPI - Mentha Protein A Protein B Gene A Gene B Score PMID P53104 P43601 ATG1 ATG18 0.183 16319894 P43601 P23291 ATG18 YCK1 0.183 16319894 P43601 P17157 ATG18 PHO85 0.183 16319894 P43601 P08431 ATG18 GAL7 0.126 11805837 P43601 P0CG63 ATG18 UBI4 0.309 21070969 P43601 P10591 ATG18 SSA1 0.126 19536198 P43601 P11484 ATG18 SSB1 0.126 19536198 P43601 P11986 ATG18 INO1 0.126 11805837 P43601 P00360 ATG18 TDH1 0.126 11805837 Q12142 P43601 ATG9 ATG18 0.454 24440502,18829864 P43601 P10592 ATG18 SSA2 0.236 16429126,19536198 P53855 P43601 ATG2 ATG18 0.976 21887408,22728243,23230146,16554755,11805837,22851171,17295840,11805826,18586673,16429126,23904270 Q06708 P43601 VAC14 ATG18 0.78 19037259,18467557 P43601 P38080 ATG18 AKL1 0.183 16319894 P43601 P38793 ATG18 TRM5 0.416 16554755 P43601 P32944 ATG18 SWE1 0.183 16319894 P43601 P00330 ATG18 ADH1 0.376 11805826,21036361,16429126 P43601 P02829 ATG18 HSP82 0.126 19536198 P43601 P02994 ATG18 TEF2 0.126 16429126 P43601 P04173 ATG18 LEU2 0.126 11805837 P43601 P05317 ATG18 RPP0 0.126 16429126 P43601 P05750 ATG18 RPS3 0.126 16429126 P43601 P07560 ATG18 SEC4 0.126 23904270 P43601 P15303 ATG18 SEC23 0.126 23904270 P43601 P21576 ATG18 VPS1 0.126 23904270 P43601 P22202 ATG18 SSA4 0.126 11805837 P43601 P25591 ATG18 VAC17 0.583 11536337,17699591,18467557 P43601 P25694 ATG18 CDC48 0.126 23904270 P43601 P32074 ATG18 SEC21 0.126 23904270 P43601 P32599 ATG18 SAC6 0.126 23904270 P43601 P32867 ATG18 SSO1 0.126 23904270 P43601 P32939 ATG18 YPT7 0.126 23904270 P43601 P34110 ATG18 VPS35 0.126 23904270 P43601 P34756 ATG18 FAB1 0.126 19037259 P43601 P38165 ATG18 RTG3 0.033 11536337 P43601 P38166 ATG18 SFT2 0.126 23904270 P43601 P38759 ATG18 VPS29 0.126 23904270 P43601 P38814 ATG18 SBE22 0.033 11536337 P43601 P38885 ATG18 AIM46 0.126 11805837 P43601 P40150 ATG18 SSB2 0.126 19536198 P43601 P40335 ATG18 PEP8 0.126 23904270 P43601 P40531 ATG18 GVP36 0.126 23904270 P43601 P40971 ATG18 LYS14 0.236 11283351 P43601 P41810 ATG18 SEC26 0.126 23904270 P43601 P42837 ATG18 FIG4 0.126 19037259 P43601 P43601 ATG18 ATG18 0.155 11805826 P43603 P43601 LSB3 ATG18 0.286 19841731 P43612 P43601 SAP155 ATG18 0.436 16554755,11805837 P47171 P43601 HIR3 ATG18 0.033 11536337 P50277 P43601 BIO3 ATG18 0.033 11536337 P53950 P43601 VAC7 ATG18 0.126 19037259 P69771 P43601 DID2 ATG18 0.126 23904270 P80667 P43601 PEX13 ATG18 0.354 19841731 Q02159 P43601 UBC7 ATG18 0.126 14690591 Q04958 P43601 NTE1 ATG18 0.033 11536337 Q05946 P43601 UTP13 ATG18 0.309 11805837 Q12418 P43601 GIS3 ATG18 0.033 11536337 Q2TAZ0 P43601 ATG2A ATG18 0.396 21887408 P43601 P14736 ATG18 RAD4 0.033 11536337 Q00362 P43601 CDC55 ATG18 0.332 11805837 P43601 P20604 ATG18 SIT4 0.332 11805837 Q08975 P43601 THI21 ATG18 0.332 11805837 P43601 P22216 ATG18 RAD53 0.033 22333915