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 GLC3 UBP9 i2d exp SSE1 UBP9 19536198 intact exp SSZ1 UBP9 19536198 intact exp TPK1 UBP9 16319894 biogrid,i2d exp SSB1 UBP9 19536198 intact exp UBP13 UBP9 16554755 intact exp UBP9 SSB2 19536198 intact exp CDC28 UBP9 16319894 biogrid exp UBP9 SKM1 16319894 biogrid,i2d exp HSL1 UBP9 16319894 biogrid,i2d exp CAJ1 UBP9 19536198 intact exp SSA2 UBP9 19536198 intact exp UBP9 SPO71 i2d exp YCK2 UBP9 16319894 biogrid,i2d exp KSP1 UBP9 16319894 biogrid,i2d exp UBP9 DJP1 19536198 intact exp FUS3 UBP9 16319894 biogrid,i2d exp TKL1 UBP9 i2d exp SFP1 UBP9 i2d exp UBP9 ATG1 16319894 biogrid,i2d exp UBP9 TOS3 i2d exp UBP9 HRK1 16319894 biogrid,i2d exp UBP9 CTI6 i2d exp UBP9 CIA1 11805837 biogrid,mint,intact,dip exp UBP9 NSE3 15752197 biogrid exp KSS1 UBP9 16319894 biogrid,i2d exp RAD53 UBP9 16319894 biogrid,i2d exp SSA1 UBP9 19536198 intact exp NPL4 UBP9 i2d exp RCK1 UBP9 16319894 biogrid,i2d exp MCK1 UBP9 16319894 biogrid,i2d exp UBP9 STE20 16319894 biogrid,i2d exp CMD1 UBP9 16554755 biogrid,i2d,mint,intact exp UBP14 UBP9 23023127 i2d exp, pred NNK1 UBP9 16319894, 23023127 biogrid,i2d exp, pred UBP9 Uncharacterized WD repeat-containing protein YOL087C 22723847,16554755, 23023127 biogrid,i2d,mint,intact exp, pred

PPI - iRefIndex UniProt A UniProt B Method PMID Interaction Type Edge type Num Participants P39967 - 11805837 - C 6 P16892 P39967 enzymatic study 16319894 direct interaction X 2 P23292 P39967 enzymatic study 16319894 direct interaction X 2 P34244 P39967 enzymatic study 16319894 direct interaction X 2 P38691 P39967 enzymatic study 16319894 direct interaction X 2 P39967 Q99247 affinity chromatography technology 22723847 physical association X 2 P39967 Q99247 pull down 22723847 direct interaction X 2 P39967 P06787 affinity chromatography technology 16554755 physical association X 2 P39967 Q99247 affinity chromatography technology 16554755 physical association X 2 P39967 P14681 enzymatic study 16319894 direct interaction X 2 P39967 P21965 enzymatic study 16319894 direct interaction X 2 P39967 Q12469 enzymatic study 16319894 direct interaction X 2 P38622 P39967 enzymatic study 16319894 direct interaction X 2 P22216 P39967 enzymatic study 16319894 direct interaction X 2 P0CG63 P39967 affinity chromatography technology 23749301 physical association X 2 P0CG63 P39967 affinity chromatography technology 19722269 physical association X 2 P39967 P00546 enzymatic study 16319894 direct interaction X 2 Q05583 P39967 affinity chromatography technology 11805837 physical association X 2 P53104 P39967 enzymatic study 16319894 direct interaction X 2 Q05541 P39967 two hybrid 15752197 direct interaction X 2 Q03497 P39967 enzymatic study 16319894 direct interaction X 2 P36003 P39967 enzymatic study 16319894 direct interaction X 2 P06244 P39967 enzymatic study 16319894 direct interaction X 2 Q08732 P39967 enzymatic study 16319894 direct interaction X 2 P39967 anti tag coimmunoprecipitation 11805837 - C 20 P39967 anti tag coimmunoprecipitation 11805837 - C 6 Q05583 P39967 anti tag coimmunoprecipitation 11805837 physical association X 2 P39967 inferred by author 16554755 association C 3 P10592 P39967 tandem affinity purification 19536198 association X 2 P32589 P39967 tandem affinity purification 19536198 association X 2 P39967 Q99247 tandem affinity purification 16554755 physical association X 2 P39967 Q99247 tandem affinity purification 16554755 physical association X 2 P39967 Q99247 tandem affinity purification 16554755 physical association X 2 P39967 Q99247 tandem affinity purification 16554755 physical association X 2 P39967 Q99247 tandem affinity purification 16554755 physical association X 2 P39967 Q99247 tandem affinity purification 16554755 physical association X 2 P39967 Q99247 tandem affinity purification 16554755 physical association X 2 P39967 P06787 tandem affinity purification 16554755 physical association X 2 P39967 P06787 tandem affinity purification 16554755 physical association X 2 P40564 P39967 tandem affinity purification 19536198 association X 2 P40150 P39967 tandem affinity purification 19536198 association X 2 P39967 anti tag coimmunoprecipitation 11805837 association C 6 P11484 P39967 tandem affinity purification 19536198 association X 2 P39101 P39967 tandem affinity purification 19536198 association X 2 P10591 P39967 tandem affinity purification 19536198 association X 2 P38788 P39967 tandem affinity purification 19536198 association X 2 P39967 mass spectrometry studies of complexes 11805837 - C 7

PPI - HINT Gene A Gene B PMID Method Quality CDC28 UBP9 16319894 0415 LC TPK1 UBP9 16319894 0415 LC KSS1 UBP9 16319894 0415 LC FUS3 UBP9 16319894 0415 LC MCK1 UBP9 16319894 0415 LC RAD53 UBP9 16319894 0415 LC YCK2 UBP9 16319894 0415 LC HSL1 UBP9 16319894 0415 LC NNK1 UBP9 16319894 0415 LC RCK1 UBP9 16319894 0415 LC KSP1 UBP9 16319894 0415 LC UBP9 ATG1 16319894 0415 LC UBP9 STE20 16319894 0415 LC UBP9 NSE3 15752197 0018 LC UBP9 HRK1 16319894 0415 LC UBP9 SKM1 16319894 0415 LC CMD1 UBP9 16554755,16554755 0676,0004 HT UBI4 UBP9 19722269 0004 LC SSA1 UBP9 19536198 0676 HT SSA2 UBP9 19536198 0676 HT SSB1 UBP9 19536198 0676 HT SSE1 UBP9 19536198 0676 HT UBP13 UBP9 16554755 0363 HT SSZ1 UBP9 19536198 0676 HT CAJ1 UBP9 19536198 0676 HT UBP9 SSB2 19536198 0676 HT UBP9 DJP1 19536198 0676 HT UBP9 INO80 26656161 0004 LC UBP9 CIA1 11805837,11805837 0004,0007 HT UBP9 Q99247 22723847,16554755,22723847,16554755 0004,0676,0096,0004 LC,HT

PPI - Mentha Protein A Protein B Gene A Gene B Score PMID P39967 P16892 UBP9 FUS3 0.183 16319894 P53104 P39967 ATG1 UBP9 0.183 16319894 P53115 P39967 INO80 UBP9 0.21 26656161 P39967 P23292 UBP9 YCK2 0.183 16319894 P39967 P0CS90 UBP9 SSC1 0.126 25792736 P39967 P00546 UBP9 CDC28 0.183 16319894 P39967 P10591 UBP9 SSA1 0.126 19536198 P39967 P10592 UBP9 SSA2 0.126 19536198 P39967 P06244 UBP9 TPK1 0.183 16319894 P39967 P06787 UBP9 CMD1 0.332 16554755 Q99247 P39967 Q99247 UBP9 0.636 16554755,22723847 P39967 P38187 UBP9 UBP13 0.126 16554755 P39967 P38691 UBP9 KSP1 0.183 16319894 P39967 P38788 UBP9 SSZ1 0.126 19536198 P39967 P11484 UBP9 SSB1 0.126 19536198 P39967 P32589 UBP9 SSE1 0.126 19536198 P39967 P39101 UBP9 CAJ1 0.126 19536198 P40150 P39967 SSB2 UBP9 0.126 19536198 Q05583 P39967 CIA1 UBP9 0.332 11805837 P39967 P36003 UBP9 NNK1 0.183 16319894 P39967 P34244 UBP9 HSL1 0.183 16319894 P40564 P39967 DJP1 UBP9 0.126 19536198 P39967 P14681 UBP9 KSS1 0.183 16319894 Q03497 P39967 STE20 UBP9 0.183 16319894 Q05541 P39967 NSE3 UBP9 0.309 15752197 P39967 P21965 UBP9 MCK1 0.183 16319894 Q08732 P39967 HRK1 UBP9 0.183 16319894 P39967 P22216 UBP9 RAD53 0.183 16319894