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 ATG3 PUF3 26493364 biogrid exp CDC19 ATG3 16429126 intact exp SSA3 ATG3 19536198 intact exp ATG3 SFI1 i2d exp NAB2 ATG3 19840948 biogrid exp ATG3 GIS2 21232131 biogrid exp ATG3 EPL1 22539722 biogrid exp HSP78 ATG3 19536198 intact exp KIN28 ATG3 21460040 biogrid exp SSB1 ATG3 16429126,19536198 intact exp ATG3 GDS1 i2d exp SSB2 ATG3 23332755 biogrid exp RPD3 ATG3 22539722 biogrid exp CCT2 ATG3 19536198 intact exp SKI3 ATG3 i2d exp TUB1 ATG3 16429126 intact exp ATG3 DJP1 19536198, 23023127 intact exp, pred ATG3 MTR10 11805826,16429126, 23023127 biogrid,mint,intact,dip exp, pred ATG3 ESA1 22539722,19303850, 23023127 biogrid exp, pred ATG3 ATG3 11805826, 23023127 mint,intact exp, pred ATG3 ATG5 17986448, 23023127 biogrid exp, pred ATG3 MYO5 19841731, 23023127 biogrid,mint,intact exp, pred KAR2 ATG3 16429126, 23023127 intact exp, pred ATG3 NUP116 11283351, 23023127 i2d,mint,intact,dip exp, pred BZZ1 ATG3 11283351, 23023127 i2d,mint,intact,dip exp, pred ATG12 ATG3 17986448,10688190,11283351,14690591, 23023127 biogrid,i2d,mint,intact,dip exp, pred PHO85 ATG3 16319894, 23023127 biogrid,i2d exp, pred ATG8 ATG3 22539722,22325599,17986448,22056771,11283351,19285500,15277523,23503366,25461810,18719252,11100732,25042851,20615880,17227760, 23023127 biogrid,i2d,mint,intact,dip exp, pred SSA1 ATG3 16429126,19536198, 23023127 intact exp, pred ATG7 ATG3 22325599,11139573,17986448,22056771,23142976,22055191,12965207,11283351,18719252,10688190,17227760, 23023127 biogrid,i2d,mint,intact,dip exp, pred SSA2 ATG3 16429126,19536198, 23023127 intact exp, pred YSC84 ATG3 19841731, 23023127 biogrid,mint,intact exp, pred UBC5 ATG3 23023127 pred ATG3 MVP1 23023127 pred ATG3 APL4 23023127 pred ATG3 TIM44 23023127 pred ATG3 VPS9 23023127 pred VPS29 ATG3 23023127 pred VPS15 ATG3 23023127 pred VPS27 ATG3 23023127 pred APS1 ATG3 23023127 pred ATG3 VAM6 23023127 pred ATG3 ATG20 23023127 pred ATG3 VPS30 23023127 pred ATG3 SGT1 23023127 pred ATG3 VPS28 23023127 pred ATG3 ATG1 23023127 pred PEP4 ATG3 23023127 pred YSP3 ATG3 23023127 pred ATG3 UBI4 23023127 pred APL3 ATG3 23023127 pred PEP5 ATG3 23023127 pred PRB1 ATG3 23023127 pred ATG3 ATG4 23023127 pred UBC1 ATG3 23023127 pred YPT53 ATG3 23023127 pred MYO3 ATG3 23023127 pred UBC4 ATG3 23023127 pred ATG3 GGA1 23023127 pred ARL1 ATG3 23023127 pred

PPI - iRefIndex UniProt A UniProt B Method PMID Interaction Type Edge type Num Participants P40344 - 11805826 - C 3 P40344 P38822 - 11283351 - X 2 P40344 P38862 - 10688190 - X 2 P40344 P38862 - 11283351 - X 2 P38316 P40344 - 11283351 - X 2 P38316 P40344 - 10688190 - X 2 P40344 Q02630 - 11283351 - X 2 P40344 P38182 - 10655498 - X 2 P40344 P38182 - 11283351 - X 2 Q99189 P40344 affinity chromatography technology 16429126 physical association X 2 Q99189 P40344 affinity chromatography technology 11805826 physical association X 2 P0CG63 P40344 affinity chromatography technology 12872131 physical association X 2 P32561 P40344 affinity chromatography technology 22539722 physical association X 2 P40150 P40344 biochemical 23332755 association X 2 P40344 P38862 x-ray crystallography 23142976 association X 2 P40344 P38862 two hybrid 12965207 direct interaction X 2 P40344 P38862 two hybrid 11139573 direct interaction X 2 P40344 P38862 affinity chromatography technology 11139573 physical association X 2 P40344 P38862 pull down 17986448 direct interaction X 2 P40344 Q12380 enzymatic study 17986448 direct interaction X 2 P40344 Q12380 pull down 17986448 direct interaction X 2 P40344 P38862 pull down 22325599 direct interaction X 2 P40344 P38862 two hybrid 11283351 direct interaction X 2 P40344 P38862 pull down 17227760 direct interaction X 2 P40344 P38862 two hybrid 18719252 direct interaction X 2 P40344 Q08649 enzymatic study 19303850 direct interaction X 2 P40344 Q04439 two hybrid 19841731 direct interaction X 2 P40344 P38862 two hybrid 11283351 direct interaction X 2 P40344 P38862 pull down 22055191 direct interaction X 2 P40344 P38862 x-ray crystallography 22055191 association X 2 P40344 P38862 pull down 22056771 direct interaction X 2 P40344 Q658J6 pull down 22056771 direct interaction X 2 P40344 P38862 two hybrid 10688190 direct interaction X 2 P40344 Q08649 enzymatic study 22539722 direct interaction X 2 P40344 Q08649 affinity chromatography technology 22539722 physical association X 2 P06242 P40344 pull down 21460040 direct interaction X 2 P38316 P40344 enzymatic study 17986448 direct interaction X 2 P38316 P40344 pull down 17986448 direct interaction X 2 P38316 P40344 two hybrid 10688190 direct interaction X 2 P43572 P40344 affinity chromatography technology 22539722 physical association X 2 P40344 P38182 affinity chromatography technology 11100732 physical association X 2 P40344 P38182 enzymatic study 23503366 direct interaction X 2 P40344 P38182 enzymatic study 17986448 direct interaction X 2 P40344 P38182 enzymatic study 22325599 direct interaction X 2 P40344 P38182 enzymatic study 15277523 direct interaction X 2 P40344 P38182 pull down 22325599 direct interaction X 2 P40344 P38182 affinity chromatography technology 25042851 physical association X 2 P40344 P38182 pull down 25461810 direct interaction X 2 P40344 P38182 two hybrid 11283351 direct interaction X 2 P40344 P38182 pull down 17227760 direct interaction X 2 P40344 P38182 two hybrid 18719252 direct interaction X 2 P40344 P38182 pull down 19285500 direct interaction X 2 P40344 P32793 two hybrid 19841731 direct interaction X 2 P40344 P17157 enzymatic study 16319894 direct interaction X 2 P40344 P38182 pull down 20615880 direct interaction X 2 P40344 P38182 two hybrid 11283351 direct interaction X 2 P40344 P38182 pull down 22056771 direct interaction X 2 P40344 P38182 affinity chromatography technology 22539722 physical association X 2 P40344 tandem affinity purification 11805826 physical association C 3 P40344 inferred by author 11805826 physical association C 3 P40344 molecular sieving 22056771 physical association C 3 P40344 molecular sieving 22056771 physical association C 3 Q99189 P40344 tandem affinity purification 11805826 physical association X 2 P40344 Q658J6 molecular sieving 22056771 direct interaction X 2 P40344 Q658J6 light scattering 22056771 direct interaction X 2 P40344 P38822 two hybrid pooling approach 11283351 physical association X 2 P40344 P38862 two hybrid pooling approach 11283351 direct interaction X 2 P40344 P38862 two hybrid 10688190 direct interaction X 2 P40344 P38862 molecular sieving 22056771 direct interaction X 2 P40344 P38862 two hybrid pooling approach 11283351 direct interaction X 2 P40344 P38862 light scattering 22056771 direct interaction X 2 P40344 P38862 cross-linking study 23142976 direct interaction X 2 P40344 P38862 coimmunoprecipitation 11139573 direct interaction X 2 P40344 P38862 molecular sieving 22056771 direct interaction X 2 P40344 P38862 cross-linking study 23142976 direct interaction X 2 P40344 P38862 two hybrid 11139573 direct interaction X 2 P38316 P40344 two hybrid 10688190 physical association X 2 P38316 P40344 two hybrid pooling approach 11283351 physical association X 2 P40344 Q02630 two hybrid pooling approach 11283351 physical association X 2 P40344 P38182 two hybrid 10655498 covalent binding X 2 P40344 P38182 two hybrid pooling approach 11283351 covalent binding X 2 P40344 P38182 molecular sieving 22056771 covalent binding X 2 P40344 P38182 coimmunoprecipitation 11100732 covalent binding X 2 P40344 P38182 comigration in sds page 23142976 covalent binding X 2 P40344 anti tag coimmunoprecipitation 25042851 association C 4 P40344 inferred by author 16429126 physical association C 4 P40344 tandem affinity purification 16429126 association C 5 P11484 P40344 tandem affinity purification 19536198 association X 2 P40344 P38862 two hybrid 10688190 physical association X 2 P40344 P38822 two hybrid fragment pooling approach 11283351 physical association X 2 P40344 P38862 two hybrid fragment pooling approach 11283351 physical association X 2 P40344 P38862 two hybrid fragment pooling approach 11283351 physical association X 2 P40344 P38862 two hybrid 12965207 physical association X 2 P40344 P38862 two hybrid 18719252 physical association X 2 P40344 P40564 tandem affinity purification 19536198 association X 2 P40344 P09435 tandem affinity purification 19536198 association X 2 P40344 Q04439 two hybrid array 19841731 physical association X 2 P10591 P40344 tandem affinity purification 19536198 association X 2 P40344 tandem affinity purification 16429126 association C 9 P40344 tandem affinity purification 11805826 association C 4 P10592 P40344 tandem affinity purification 19536198 association X 2 P38316 P40344 two hybrid 10688190 physical association X 2 P38316 P40344 two hybrid fragment pooling approach 11283351 physical association X 2 P38316 P40344 two hybrid array 14690591 physical association X 2 P39076 P40344 tandem affinity purification 19536198 association X 2 P40344 Q02630 two hybrid fragment pooling approach 11283351 physical association X 2 P40344 P38182 two hybrid fragment pooling approach 11283351 physical association X 2 P40344 P40344 tandem affinity purification 11805826 physical association X 2 P40344 P38182 two hybrid 18719252 physical association X 2 P40344 P38182 biochemical 19285500 direct interaction X 2 P40344 P33416 tandem affinity purification 19536198 association X 2 P40344 P32793 two hybrid array 19841731 physical association X 2 P40344 P38822 two hybrid 11283351 - X 2 P40344 P38862 two hybrid 10688190 - X 2 P40344 P38862 two hybrid 11283351 - X 2 P40344 P38862 two hybrid 11283351 - X 2 P40344 mass spectrometry studies of complexes 11805826 - C 5 P40344 mass spectrometry studies of complexes 11805826 - C 5 P38316 P40344 two hybrid 11283351 - X 2 P38316 P40344 two hybrid 10688190 - X 2 P40344 Q02630 two hybrid 11283351 - X 2 P40344 P38182 two hybrid 11283351 - X 2 P40344 P38182 two hybrid 10655498 - X 2

PPI - HINT Gene A Gene B PMID Method Quality PHO85 ATG3 16319894 0415 LC YSC84 ATG3 19841731,19841731 0397,0018 HT ATG8 ATG3 15277523,17986448,23503366,19285500,19285500,11100732,11283351,11283351,23142976,10655498,22325599,18719252,11283351,22056771,22056771,11100732,22325599 0415,0415,0415,0096,0401,0004,0398,0399,0808,0018,0096,0018,0018,0096,0071,0019,0415 LC,HT ATG12 ATG3 17986448,11283351,11283351,11283351,17986448,10688190,10688190,14690591 0415,0018,0399,0398,0096,0397,0018,0397 LC,HT BZZ1 ATG3 11283351,11283351,11283351 0018,0399,0398 HT ATG7 ATG3 22055190,17986448,11139573,22055191,11139573,12965207,22055191,11139573,11283351,10688190,10688190,11283351,17986448,18719252,23142976,22056771,11283351,22056771,22056771,23142976 0114,0415,0018,0096,0004,0018,0114,0019,0398,0397,0018,0399,0096,0018,0030,0067,0018,0096,0071,0114 LC,HT SSB2 ATG3 23332755 0401 LC ATG3 NUP116 11283351,11283351,11283351 0018,0399,0398 HT ATG3 MYO5 19841731,19841731 0397,0018 HT ATG3 ESA1 22539722,22539722,19303850 0004,0415,0415 LC ATG3 ATG5 17986448,17986448 0096,0415 LC CDC19 ATG3 16429126 0363 HT KIN28 ATG3 21460040 0096 LC SSA3 ATG3 19536198 0676 HT TUB1 ATG3 16429126 0363 HT SSA1 ATG3 19536198,16429126 0676,0676 HT SSA2 ATG3 19536198,16429126 0676,0676 HT SSB1 ATG3 19536198,16429126 0676,0676 HT KAR2 ATG3 16429126 0676 HT NAB2 ATG3 19840948 0004 LC RPD3 ATG3 22539722 0004 LC HSP78 ATG3 19536198 0676 HT ATG8 ATG3 19285500,19285500,20615880,11100732,22539722,25461810,25042851,22325599,25042851,22056771,22056771,17227760,11100732,22325599 0096,0401,0096,0004,0004,0096,0004,0096,0007,0096,0071,0096,0019,0415 LC ATG12 ATG3 17986448,17986448 0415,0096 LC ATG7 ATG3 17986448,11139573,22055191,11139573,22055191,11139573,17986448,22325599,22056771,22056771,22056771,17227760 0415,0018,0096,0004,0114,0019,0096,0096,0067,0096,0071,0096 LC CCT2 ATG3 19536198 0676 HT SSB2 ATG3 23332755 0401 LC ATG3 ATG3 11805826,11805826 0676,0007 HT ATG3 DJP1 19536198 0676 HT ATG3 EPL1 22539722 0004 LC ATG3 ESA1 22539722,22539722 0004,0415 LC ATG3 ATG5 17986448,17986448 0096,0415 LC ATG3 MTR10 16429126,11805826,11805826,11805826,16429126,16429126 0676,0676,0004,0007,0004,0363 HT

PPI - Mentha Protein A Protein B Gene A Gene B Score PMID P40344 P17157 ATG3 PHO85 0.183 16319894 P40344 P09435 ATG3 SSA3 0.126 19536198 P40344 P06242 ATG3 KIN28 0.183 21460040 P40344 P38316 ATG3 ATG12 0.765 10688190,14690591,17986448,11283351 P40344 P10592 ATG3 SSA2 0.236 16429126,19536198 P40344 P10591 ATG3 SSA1 0.236 16429126,19536198 Q12380 P40344 ATG5 ATG3 0.523 17986448 P40344 P38182 ATG3 ATG8 0.99 25461810,20615880,22056771,23503366,11100732,10655498,22325599,15277523,18719252,22539722,19285500,25042851,17986448,11283351 P40344 P38862 ATG3 ATG7 0.974 10688190,22056771,17986448,11283351,12965207,23142976,11139573,22325599,18719252,22055191 P40344 P32505 ATG3 NAB2 0.126 19840948 P40344 P32793 ATG3 YSC84 0.354 19841731 P40344 P40150 ATG3 SSB2 0.126 23332755 P40344 P00549 ATG3 CDC19 0.126 16429126 P40344 P09733 ATG3 TUB1 0.126 16429126 P40344 P11484 ATG3 SSB1 0.236 16429126,19536198 P40344 P16474 ATG3 KAR2 0.126 16429126 P40344 P32561 ATG3 RPD3 0.21 22539722 P40344 P33416 ATG3 HSP78 0.126 19536198 P40344 P38822 ATG3 BZZ1 0.21 11283351 P40344 P39076 ATG3 CCT2 0.126 19536198 P40344 P40344 ATG3 ATG3 0.155 11805826 P43572 P40344 EPL1 ATG3 0.21 22539722 Q02630 P40344 NUP116 ATG3 0.236 11283351 Q04439 P40344 MYO5 ATG3 0.376 19841731 Q08649 P40344 ESA1 ATG3 0.554 22539722,19303850 Q99189 P40344 MTR10 ATG3 0.539 11805826,16429126 Q9GZQ8 P40344 MAP1LC3B ATG3 0.309 22056771 P40564 P40344 DJP1 ATG3 0.126 19536198 P53849 P40344 GIS2 ATG3 0.126 21232131 Q07807 P40344 PUF3 ATG3 0.126 26493364