| CDC48 | YDL126C | AAA ATPase with protein-unfoldase activity | physical | 2 | 2 | 2 | Affinity Capture-MS, Two-hybrid | 
            
                | FKH1 | YIL131C | Forkhead family transcription factor | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | MED4 | YOR174W | Subunit of the RNA polymerase II mediator complex | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | SWI5 | YDR146C | Transcription factor that recruits Mediator and Swi/Snf complexes | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | CCR4 | YAL021C | Component of the CCR4-NOT transcriptional complex | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | NAB2 | YGL122C | Nuclear polyadenylated RNA-binding protein | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | URA7 | YBL039C | Major CTP synthase isozyme (see also URA8) | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | ARP3 | YJR065C | Essential component of the Arp2/3 complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | DHH1 | YDL160C | Cytoplasmic DEAD-box helicase and mRNA decapping activator | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | NPL4 | YBR170C | Substrate-recruiting cofactor of the Cdc48p-Npl4p-Ufd1p segregase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PST2 | YDR032C | FMN-dependent NAD(P)H:quinone oxidoreductase | physical | 1 | 1 | 1 | PCA | 
            
                | PMA1 | YGL008C | Plasma membrane P2-type H+-ATPase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | GPA2 | YER020W | Nucleotide binding alpha subunit of the heterotrimeric G protein | physical | 1 | 1 | 1 | PCA | 
            
                | MAK11 | YKL021C | Protein involved in an early step of 60S ribosomal subunit biogenesis | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | TTI1 | YKL033W | Subunit of the ASTRA complex, involved in chromatin remodeling | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | DAL81 | YIR023W | Positive regulator of genes in multiple nitrogen degradation pathways | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MCM3 | YEL032W | Protein involved in DNA replication | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | RSM19 | YNR037C | Mitochondrial ribosomal protein of the small subunit | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | SFK1 | YKL051W | Protein that regulates phospholipid asymmetry at plasma membrane | physical | 1 | 1 | 1 | PCA | 
            
                | MID2 | YLR332W | O-glycosylated plasma membrane protein | physical | 1 | 1 | 1 | PCA | 
            
                | BCS1 | YDR375C | Protein translocase and chaperone required for Complex III assembly | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | ERF2 | YLR246W | Subunit of a palmitoyltransferase | physical | 1 | 1 | 1 | Biochemical Activity | 
            
                | HNM1 | YGL077C | Plasma membrane transporter for choline, ethanolamine, and carnitine | physical | 1 | 1 | 1 | PCA | 
            
                | RIM1 | YCR028C-A | ssDNA-binding protein essential for mitochondrial genome maintenance | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | UME6 | YDR207C | Rpd3L histone deacetylase complex subunit | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | SLF1 | YDR515W | RNA binding protein that associates with polysomes | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | GIS2 | YNL255C | Translational activator for mRNAs with internal ribosome entry sites | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | FMP45 | YDL222C | Integral membrane protein localized to mitochondria | physical | 1 | 1 | 1 | PCA | 
            
                | MUP1 | YGR055W | High affinity methionine permease | physical | 1 | 1 | 1 | PCA | 
            
                | WSC2 | YNL283C | Sensor-transducer of the stress-activated PKC1-MPK1 signaling pathway | physical | 1 | 1 | 1 | PCA | 
            
                | PFA4 | YOL003C | Palmitoyltransferase with autoacylation activity | physical | 1 | 1 | 1 | Biochemical Activity | 
            
                | PFA5 | YDR459C | Palmitoyltransferase with autoacylation activity | physical | 1 | 1 | 1 | Biochemical Activity | 
            
                | CBP4 | YGR174C | Mitochondrial protein required for assembly of cytochrome bc1 complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | TAX4 | YJL083W | EH domain-containing protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PET20 | YPL159C | Mitochondrial protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | YBR238C | YBR238C | Mitochondrial membrane protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | YER079W | YER079W | Putative protein of unknown function | genetic | 1 | 1 | 1 | Negative Genetic |