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 PEX4 ORC3 i2d exp PEX4 SSB2 23332755 biogrid exp SSA1 PEX4 19536198 intact exp PEX4 NAB2 19840948 biogrid exp PEX4 DML1 11283351 i2d,mint,intact,dip exp PEX4 PUF3 23409723 biogrid exp PEX4 NAM7 18087042 biogrid exp SSB1 PEX4 19536198 intact exp SAM35 PEX4 14690591 intact exp UBA1 PEX4 22085930,9341106 biogrid exp PEX4 CCT4 19536198 intact exp PEX4 PEX11 22615397,18467557, 23023127 biogrid,i2d,mint,intact exp, pred PEX4 PEX12 22471590,24034674,25162638, 23023127 biogrid exp, pred PEX4 PEX4 23896733,22085930,18644345,12876220,25162638, 23023127 biogrid,dip exp, pred PEX4 PEX22 23896733,22085930,doi:10.1038/emboj.2011.411,12876220,19017643,18719252, 23023127 biogrid,mint,intact,dip exp, pred PEX4 PEX2 19687296,22471590, 23023127 biogrid exp, pred PEX4 PEX10 22471590,12876220,24034674, 23023127 biogrid,mint,intact,dip exp, pred CDC34 PEX4 23023127 pred PEX4 UBC11 23023127 pred UBC5 PEX4 23023127 pred PEX4 UBP6 23023127 pred PEX4 PRP19 23023127 pred RAD18 PEX4 23023127 pred PEX4 PEX7 23023127 pred PEX1 PEX4 23023127 pred PEX3 PEX4 23023127 pred PEX4 PEX14 23023127 pred UBC4 PEX4 23023127 pred PEX4 PEX13 23023127 pred PEX4 UBC7 23023127 pred PEX4 HRT1 23023127 pred PEX4 PEX5 23023127 pred PEX4 TUL1 23023127 pred PEX4 UBC13 23023127 pred PEX4 UBC9 23023127 pred PEX4 UBX7 23023127 pred PEX4 RUB1 23023127 pred UBC8 PEX4 23023127 pred PEX4 UBX5 23023127 pred PEX4 MPE1 23023127 pred PEX4 DMA2 23023127 pred PEX4 RSP5 23023127 pred PEX4 UBI4 23023127 pred PEX4 PEX6 23023127 pred PEX4 UBC12 23023127 pred PEX4 DMA1 23023127 pred PEX4 UBC6 23023127 pred RAD6 PEX4 23023127 pred PEX4 SMT3 23023127 pred PEX4 HUB1 23023127 pred PEX4 UBX6 23023127 pred PEX4 MMS2 23023127 pred UBC1 PEX4 23023127 pred PEX4 RAD23 23023127 pred

PPI - iRefIndex UniProt A UniProt B Method PMID Interaction Type Edge type Num Participants P29340 Q03652 - 11283351 - X 2 P29340 P29340 enzymatic study 22085930 direct interaction X 2 P29340 P22515 enzymatic study 22085930 direct interaction X 2 P29340 P29340 enzymatic study 23896733 direct interaction X 2 P29340 P29340 enzymatic study 25162638 direct interaction X 2 P29340 P32800 pull down 22471590 direct interaction X 2 P29340 Q05568 pull down 22471590 direct interaction X 2 P29340 Q05568 pull down 24034674 direct interaction X 2 P29340 P22515 enzymatic study 9341106 direct interaction X 2 P29340 Q12462 protein complementation assay 18467557 direct interaction X 2 P29340 P29340 enzymatic study 18644345 direct interaction X 2 P29340 P29340 protein complementation assay 12876220 direct interaction X 2 P29340 Q05568 protein complementation assay 12876220 direct interaction X 2 P29340 P32800 affinity chromatography technology 19687296 physical association X 2 P29340 Q12462 protein complementation assay 22615397 direct interaction X 2 P29340 P39718 two hybrid 22085930 direct interaction X 2 P29340 P39718 pull down 22085930 direct interaction X 2 P29340 P39718 x-ray crystallography 23896733 association X 2 P29340 Q04370 pull down 25162638 direct interaction X 2 P29340 Q04370 pull down 22471590 direct interaction X 2 P29340 Q04370 pull down 24034674 direct interaction X 2 P29340 P40150 biochemical 23332755 association X 2 P29340 P39718 two hybrid 18719252 direct interaction X 2 P29340 P39718 two hybrid 19017643 direct interaction X 2 P29340 P39718 protein complementation assay 12876220 direct interaction X 2 P29340 P39718 x-ray crystallography 22085930 association X 2 P29340 P39718 affinity chromatography technology 22085930 physical association X 2 P29340 Q03652 two hybrid pooling approach 11283351 physical association X 2 P29340 P29340 ubiquitin reconstruction 12876220 physical association Y 1 P29340 Q05568 coimmunoprecipitation 12876220 physical association X 2 P29340 Q05568 ubiquitin reconstruction 12876220 physical association X 2 P29340 Q05568 two hybrid 12876220 physical association X 2 P29340 P39718 ubiquitin reconstruction 12876220 physical association X 2 P29340 Q03652 two hybrid fragment pooling approach 11283351 physical association X 2 P29340 Q05568 ubiquitin reconstruction 12876220 physical association X 2 P29340 Q12462 dihydrofolate reductase reconstruction 18467557 physical association X 2 P29340 P39078 tandem affinity purification 19536198 association X 2 P29340 P39718 ubiquitin reconstruction 12876220 physical association X 2 P29340 P14693 two hybrid array 14690591 physical association X 2 P29340 P39718 two hybrid 18719252 physical association X 2 P29340 P10591 tandem affinity purification 19536198 association X 2 P29340 P11484 tandem affinity purification 19536198 association X 2 P29340 P39718 isothermal titration calorimetry 22085930 direct interaction X 2 P29340 P39718 circular dichroism 22085930 direct interaction X 2 P29340 P39718 anti tag coimmunoprecipitation 22085930 physical association X 2 P29340 P39718 blue native page 22085930 direct interaction X 2 P29340 P39718 isothermal titration calorimetry 22085930 direct interaction X 2 P29340 P39718 isothermal titration calorimetry 22085930 direct interaction X 2 P29340 P39718 x-ray crystallography 22085930 direct interaction X 2 P29340 P39718 two hybrid 22085930 physical association X 2 P29340 Q03652 two hybrid 11283351 - X 2 P29340 P33336 interaction detection method 14764870 - X 2 P29340 P50112 interaction detection method 14764870 - X 2 P29340 P47124 interaction detection method 14764870 - X 2 P29340 P38631 interaction detection method 14764870 - X 2

PPI - HINT Gene A Gene B PMID Method Quality SAM35 PEX4 14690591 0397 LC UBA1 PEX4 22085930,9341106 0415,0415 LC PEX4 PEX4 12876220,18644345,12876220,23896733,25162638,22085930 0090,0415,0112,0415,0415,0415 LC PEX4 PEX22 19017643,22085930,22085930,22085930,23896733,22085930,22085930,18719252,PDB_2Y9P,12876220,22085930,22085930,12876220,22085930 0018,0007,0114,0004,0114,0018,0016,0018,0114,0112,0276,0096,0090,0065 LC,HT PEX4 SSB2 23332755 0401 LC PEX4 DML1 11283351,11283351,11283351 0018,0399,0398 HT PEX4 PEX10 12876220,12876220,12876220,12876220 0090,0019,0018,0112 LC PEX4 PEX11 18467557,18467557,22615397 0111,0090,0090 HT,LC SSA1 PEX4 19536198 0676 HT SSB1 PEX4 19536198 0676 HT PEX4 NAB2 19840948 0004 LC PEX4 PEX2 22471590,19687296 0096,0004 LC PEX4 PEX5 17550898 0004 LC PEX4 CCT4 19536198 0676 HT PEX4 PEX22 22085930,22085930,22085930,22085930,22085930,22085930,22085930,22085930 0007,0114,0004,0018,0016,0276,0096,0065 LC PEX4 SSB2 23332755 0401 LC PEX4 PEX12 25162638,24034674,22471590 0096,0096,0096 LC PEX4 PEX10 22471590,24034674 0096,0096 LC

PPI - Mentha Protein A Protein B Gene A Gene B Score PMID Q12462 P29340 PEX11 PEX4 0.126 18467557 P29340 P11484 PEX4 SSB1 0.126 19536198 P32800 P29340 PEX2 PEX4 0.454 19687296,22471590 Q05568 P29340 PEX10 PEX4 0.692 12876220,24034674,22471590 Q04370 P29340 PEX12 PEX4 0.671 25162638,24034674,22471590 P29340 P10591 PEX4 SSA1 0.126 19536198 P29340 P14693 PEX4 SAM35 0.126 14690591 P29340 P22515 PEX4 UBA1 0.523 22085930,9341106 P29340 P29340 PEX4 PEX4 0.794 23896733,12876220,22085930,18644345,25162638 P39078 P29340 CCT4 PEX4 0.126 19536198 Q03652 P29340 DML1 PEX4 0.21 11283351 P30771 P29340 NAM7 PEX4 0.126 18087042 P32505 P29340 NAB2 PEX4 0.126 19840948 P39718 P29340 PEX22 PEX4 0.993 19017643,23896733,12876220,22085930,18719252 P40150 P29340 SSB2 PEX4 0.126 23332755 Q07807 P29340 PUF3 PEX4 0.126 23409723