| FKH1 | YIL131C | Forkhead family transcription factor | regulation | 3 | 2 | 3 | chromatin immunoprecipitation-chip evidence, chromatin immunoprecipitation-chip evidence, ChEC-Seq experiments | 
            
                | WHI3 | YNL197C | RNA binding protein that modulates mRNA stability | physical | 2 | 2 | 2 | Protein-RNA, Affinity Capture-RNA | 
            
                | DHH1 | YDL160C | Cytoplasmic DEAD-box helicase and mRNA decapping activator | physical | 2 | 1 | 2 | Affinity Capture-RNA, Affinity Capture-RNA | 
            
                | BFR1 | YOR198C | Component of mRNP complexes associated with polyribosomes | genetic | 2 | 1 | 1 | Negative Genetic, Negative Genetic | 
            
                | OPI3 | YJR073C | Methylene-fatty-acyl-phospholipid synthase | genetic | 2 | 1 | 1 | Positive Genetic, Positive Genetic | 
            
                | GCN5 | YGR252W | Catalytic subunit of ADA and SAGA histone acetyltransferase complexes | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | ACE2 | YLR131C | Transcription factor required for septum destruction after cytokinesis | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | FKH2 | YNL068C | Forkhead family transcription factor | regulation | 1 | 1 | 1 | ChEC-Seq experiments | 
            
                | GCR1 | YPL075W | Transcriptional activator of genes involved in glycolysis | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | HFI1 | YPL254W | Adaptor protein required for structural integrity of the SAGA complex | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | MED2 | YDL005C | Subunit of the RNA polymerase II mediator complex | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | SPT20 | YOL148C | Subunit of the SAGA transcriptional regulatory complex | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | XBP1 | YIL101C | Transcriptional repressor | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | RAP1 | YNL216W | Essential DNA-binding transcription regulator that binds many loci | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | STP1 | YDR463W | Transcription factor | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | YAP1 | YML007W | Basic leucine zipper (bZIP) transcription factor | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | SIN4 | YNL236W | Subunit of the RNA polymerase II mediator complex | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | HSF1 | YGL073W | Trimeric heat shock transcription factor | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | SPT3 | YDR392W | Subunit of the SAGA and SAGA-like transcriptional regulatory complexes | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | YAP5 | YIR018W | Basic leucine zipper (bZIP) iron-sensing transcription factor | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | CST6 | YIL036W | Basic leucine zipper (bZIP) transcription factor from ATF/CREB family | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | TUP1 | YCR084C | General repressor of transcription in complex with Cyc8p | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | SRB2 | YHR041C | Subunit of the RNA polymerase II mediator complex | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | SWI5 | YDR146C | Transcription factor that recruits Mediator and Swi/Snf complexes | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | RPH1 | YER169W | JmjC domain-containing histone demethylase | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | ACT1 | YFL039C | Actin, structural protein in cytoskeleton | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | CCR4 | YAL021C | Component of the CCR4-NOT transcriptional complex | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | CDC11 | YJR076C | Component of the septin ring that is required for cytokinesis | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | AIM3 | YBR108W | Protein that inhibits barbed-end actin filament elongation | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | BFR1 | YOR198C | Component of mRNP complexes associated with polyribosomes | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | ASH1 | YKL185W | Component of the Rpd3L histone deacetylase complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | AIM44 | YPL158C | Regulator of Cdc42p and Rho1p | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | SRS2 | YJL092W | DNA helicase and DNA-dependent ATPase | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | SST2 | YLR452C | GTPase-activating protein for Gpa1p | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | 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 | 
            
                | SRO9 | YCL037C | Cytoplasmic RNA-binding protein | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | SBP1 | YHL034C | Protein that binds eIF4G and has a role in repression of translation | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | PUF2 | YPR042C | PUF family mRNA-binding protein | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | ISW1 | YBR245C | ATPase subunit of imitation-switch (ISWI) class chromatin remodelers | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | MPT5 | YGL178W | mRNA-binding protein of the PUF family | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | PPA2 | YMR267W | Mitochondrial inorganic pyrophosphatase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | HOF1 | YMR032W | F-BAR protein that regulates actin cytoskeleton organization | genetic | 1 | 1 | 1 | Synthetic Rescue | 
            
                | FAB1 | YFR019W | 1-phosphatidylinositol-3-phosphate 5-kinase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | SNC2 | YOR327C | Vesicle membrane receptor protein (v-SNARE) | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | RPO21 | YDL140C | RNA polymerase II largest subunit B220 | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | RLI1 | YDR091C | Essential Fe-S protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | STT3 | YGL022W | Catalytic subunit of the oligosaccharyltransferase complex of the ER l | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PRP43 | YGL120C | RNA helicase in the DEAH-box family | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | NOP2 | YNL061W | rRNA m5C methyltransferase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | RPC34 | YNR003C | RNA polymerase III subunit C34 | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | RPB2 | YOR151C | RNA polymerase II second largest subunit B150 | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MDM10 | YAL010C | Subunit of both the ERMES and the SAM complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | ELO2 | YCR034W | Fatty acid elongase, involved in sphingolipid biosynthesis | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | SLM3 | YDL033C | tRNA-specific 2-thiouridylase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | NUR1 | YDL089W | Protein involved in regulation of mitotic exit | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | QRI7 | YDL104C | Protein involved in threonylcarbamoyl adenosine biosynthesis | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PET122 | YER153C | Mitochondrial translational activator specific for the COX3 mRNA | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | KAP122 | YGL016W | Karyopherin beta | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | SNF6 | YHL025W | Subunit of the SWI/SNF chromatin remodeling complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | IRE1 | YHR079C | Serine-threonine kinase and endoribonuclease | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | FLX1 | YIL134W | Mitochondrial flavin adenine dinucleotide transporter | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MDM35 | YKL053C-A | Mitochondrial intermembrane space protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MMS22 | YLR320W | Subunit of E3 ubiquitin ligase complex involved in replication repair | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | ELO3 | YLR372W | Elongase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | IRA2 | YOL081W | GTPase-activating protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | HMI1 | YOL095C | Mitochondrial inner membrane localized ATP-dependent DNA helicase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MNE1 | YOR350C | Protein involved in splicing Group I aI5-beta intron from COX1 mRNA | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MSC6 | YOR354C | Multicopy suppressor of HER2 involved in mitochondrial translation | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | RTC6 | YPL183W-A | Protein involved in translation | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | LEA1 | YPL213W | Component of U2 snRNP complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | YME1 | YPR024W | Catalytic subunit of i-AAA protease complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | SPE3 | YPR069C | Spermidine synthase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MSS18 | YPR134W | Nuclear encoded protein needed for splicing of mitochondrial intron | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | CYK3 | YDL117W | SH3-domain protein located in the bud neck and cytokinetic actin ring | genetic | 1 | 1 | 1 | Synthetic Rescue | 
            
                | COA4 | YLR218C | Twin Cx(9)C protein involved in cytochrome c oxidase organization | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | COX23 | YHR116W | Protein that functions in mitochondrial copper homeostasis | genetic | 1 | 1 | 1 | Negative Genetic |