| PUF3 | YLL013C | Protein of the mitochondrial outer surface | physical | 4 | 1 | 4 | Affinity Capture-RNA, Affinity Capture-RNA, Affinity Capture-RNA, Affinity Capture-RNA | 
            
                | FKH1 | YIL131C | Forkhead family transcription factor | regulation | 3 | 2 | 3 | chromatin immunoprecipitation-chip evidence, chromatin immunoprecipitation-chip evidence, chromatin immunoprecipitation- exonuclease evidence | 
            
                | GCN5 | YGR252W | Catalytic subunit of ADA and SAGA histone acetyltransferase complexes | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | FKH2 | YNL068C | Forkhead family transcription factor | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | MED2 | YDL005C | Subunit of the RNA polymerase II mediator complex | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | MSN2 | YMR037C | Stress-responsive transcriptional activator | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | RAP1 | YNL216W | Essential DNA-binding transcription regulator that binds many loci | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | YAP1 | YML007W | Basic leucine zipper (bZIP) transcription factor | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | SUA7 | YPR086W | Transcription factor TFIIB | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | CSL4 | YNL232W | Exosome non-catalytic core component | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | CCR4 | YAL021C | Component of the CCR4-NOT transcriptional complex | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | AHC1 | YOR023C | Subunit of the Ada histone acetyltransferase complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | TAF12 | YDR145W | Subunit (61/68 kDa) of TFIID and SAGA complexes | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | HEK2 | YBL032W | RNA binding protein involved in asymmetric localization of ASH1 mRNA | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | NAB2 | YGL122C | Nuclear polyadenylated RNA-binding protein | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | MPT5 | YGL178W | mRNA-binding protein of the PUF family | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | GLC7 | YER133W | Type 1 S/T protein phosphatase (PP1) catalytic subunit | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | LCB1 | YMR296C | Component of serine palmitoyltransferase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | NPL3 | YDR432W | RNA-binding protein | genetic | 1 | 1 | 1 | Synthetic Rescue | 
            
                | MED4 | YOR174W | Subunit of the RNA polymerase II mediator complex | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | IMG1 | YCR046C | Mitochondrial ribosomal protein of the large subunit | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | RPN4 | YDL020C | Transcription factor that stimulates expression of proteasome genes | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | SIW14 | YNL032W | Inositol phosphatase involved in inositol pyrophosphate metabolism | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | VAM3 | YOR106W | Syntaxin-like vacuolar t-SNARE | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | RPS10A | YOR293W | Protein component of the small (40S) ribosomal subunit | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | RPL21B | YPL079W | Ribosomal 60S subunit protein L21B | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | RSC58 | YLR033W | Component of the RSC chromatin remodeling complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MRS6 | YOR370C | Rab escort protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | SGV1 | YPR161C | Cyclin (Bur2p)-dependent protein kinase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | FMP23 | YBR047W | Putative protein of unknown function | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | GDT1 | YBR187W | Calcium and manganese transporter with higher affinity for Ca2+ | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MRPL35 | YDR322W | Mitochondrial ribosomal protein of the large subunit | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PIB2 | YGL023C | Phosphatidylinositol 3-phosphate binding protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | YBP2 | YGL060W | Central kinetochore associated protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | KXD1 | YGL079W | Subunit of the BLOC-1 complex involved in endosomal maturation | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | OCA5 | YHL029C | Cytoplasmic protein required for replication of Brome mosaic virus | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | NDT80 | YHR124W | Meiosis-specific transcription factor | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MRS1 | YIR021W | Splicing protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MGM101 | YJR144W | Protein with a role in mitochondrial DNA recombinational repair | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | HCS1 | YKL017C | Hexameric DNA polymerase alpha-associated DNA helicase A | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | YLL006W-A | YLL006W-A | Putative protein of unknown function | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | QRI5 | YLR204W | Mitochondrial inner membrane protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | SGF29 | YCL010C | Component of the HAT/Core module of the SAGA, SLIK, and ADA complexes | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MOG1 | YJR074W | Conserved nuclear protein that interacts with GTP-Gsp1p | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PHO23 | YNL097C | Component of the Rpd3L histone deacetylase complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | FAR11 | YNL127W | Protein involved in recovery from cell cycle arrest | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | LSM7 | YNL147W | Lsm (Like Sm) protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | RIM20 | YOR275C | Protein involved in proteolytic activation of Rim101p | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | YTA6 | YPL074W | Putative ATPase of the CDC48/PAS1/SEC18 (AAA) family | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | FUM1 | YPL262W | Fumarase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | TRM12 | YML005W | S-adenosylmethionine-dependent methyltransferase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PEX9 | YMR018W | Peroxisomal membrane signal receptor for peroxisomal matrix proteins | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | VPS68 | YOL129W | Vacuolar membrane protein of unknown function | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MGM1 | YOR211C | Mitochondrial GTPase, present in complex with Ugo1p and Fzo1p | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | KAR9 | YPL269W | Spindle positioning factor | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | HSP32 | YPL280W | Possible chaperone and cysteine protease | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | YPR159C-A | YPR159C-A | Protein of unknown function | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | BFR1 | YOR198C | Component of mRNP complexes associated with polyribosomes | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | CRS1 | YNL247W | Cysteinyl-tRNA synthetase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | BRR6 | YGL247W | Essential nuclear envelope integral membrane protein | genetic | 1 | 1 | 1 | Negative Genetic |