| CDC28 | YBR160W | Cyclin-dependent kinase (CDK) catalytic subunit | physical | 3 | 1 | 3 | Biochemical Activity, Biochemical Activity, Biochemical Activity | 
            
                | AIM44 | YPL158C | Regulator of Cdc42p and Rho1p | genetic | 3 | 1 | 2 | Negative Genetic, Negative Genetic, Negative Genetic | 
            
                | CDH1 | YGL003C | Activator of anaphase-promoting complex/cyclosome (APC/C) | physical | 3 | 3 | 1 | Two-hybrid, Affinity Capture-Western, Biochemical Activity | 
            
                | FKH1 | YIL131C | Forkhead family transcription factor | regulation | 2 | 2 | 2 | chromatin immunoprecipitation-chip evidence, ChEC-Seq experiments | 
            
                | FKH2 | YNL068C | Forkhead family transcription factor | regulation | 2 | 2 | 2 | chromatin immunoprecipitation-chip evidence, ChEC-Seq experiments | 
            
                | BEM1 | YBR200W | Protein containing SH3-domains | genetic | 2 | 1 | 2 | Negative Genetic, Negative Genetic | 
            
                | CIK1 | YMR198W | Kinesin-associated protein | genetic | 2 | 1 | 2 | Negative Genetic, Negative Genetic | 
            
                | BUB1 | YGR188C | Protein kinase involved in the cell cycle checkpoint into anaphase | genetic | 2 | 1 | 2 | Negative Genetic, Negative Genetic | 
            
                | MPT5 | YGL178W | mRNA-binding protein of the PUF family | physical | 2 | 1 | 2 | Affinity Capture-RNA, Affinity Capture-RNA | 
            
                | SFP1 | YLR403W | Regulates transcription of ribosomal protein and biogenesis genes | 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 | 
            
                | YAP6 | YDR259C | Basic leucine zipper (bZIP) transcription factor | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | CDC28 | YBR160W | Cyclin-dependent kinase (CDK) catalytic subunit | regulation | 1 | 1 | 1 | quantitative mass spectrometry evidence | 
            
                | AFT1 | YGL071W | Transcription factor involved in iron utilization and homeostasis | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | SPT16 | YGL207W | Subunit of the heterodimeric FACT complex (Spt16p-Pob3p) | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | ACT1 | YFL039C | Actin, structural protein in cytoskeleton | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | DHH1 | YDL160C | Cytoplasmic DEAD-box helicase and mRNA decapping activator | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | HST1 | YOL068C | NAD(+)-dependent histone deacetylase | physical | 1 | 1 | 1 | Affinity Capture-Western | 
            
                | HST1 | YOL068C | NAD(+)-dependent histone deacetylase | genetic | 1 | 1 | 1 | Synthetic Rescue | 
            
                | COG3 | YER157W | Essential component of the conserved oligomeric Golgi complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | CMD1 | YBR109C | Calmodulin | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PRP28 | YDR243C | Pre-mRNA splicing factor | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | RPD3 | YNL330C | Histone deacetylase, component of both the Rpd3S and Rpd3L complexes | physical | 1 | 1 | 1 | Affinity Capture-Western | 
            
                | RPD3 | YNL330C | Histone deacetylase, component of both the Rpd3S and Rpd3L complexes | genetic | 1 | 1 | 1 | Synthetic Rescue | 
            
                | MNN10 | YDR245W | Subunit of a Golgi mannosyltransferase complex | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | SNF1 | YDR477W | AMP-activated S/T protein kinase | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | SSE1 | YPL106C | ATPase component of heat shock protein Hsp90 chaperone complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PTC1 | YDL006W | Type 2C protein phosphatase (PP2C) | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PHO85 | YPL031C | Cyclin-dependent kinase | physical | 1 | 1 | 1 | Biochemical Activity | 
            
                | ATG17 | YLR423C | Scaffold protein responsible for phagophore assembly site organization | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | DUN1 | YDL101C | Cell-cycle checkpoint S/T protein kinase | genetic | 1 | 1 | 1 | Synthetic Growth Defect | 
            
                | PBR1 | YNL181W | Putative oxidoreductase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MRS6 | YOR370C | Rab escort protein | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | SGS1 | YMR190C | RecQ family nucleolar DNA helicase | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | HOM3 | YER052C | Aspartate kinase (L-aspartate 4-P-transferase) | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | SWI5 | YDR146C | Transcription factor that recruits Mediator and Swi/Snf complexes | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | OMS1 | YDR316W | Protein integral to the mitochondrial membrane | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | BUB3 | YOR026W | Kinetochore checkpoint WD40 repeat protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | CDH1 | YGL003C | Activator of anaphase-promoting complex/cyclosome (APC/C) | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | BIR1 | YJR089W | Subunit of chromosomal passenger complex (CPC) | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | CHA4 | YLR098C | DNA binding transcriptional activator | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | LEU3 | YLR451W | Zinc-knuckle transcription factor, repressor and activator | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | RTG3 | YBL103C | bHLH/Zip transcription factor for retrograde (RTG) and TOR pathways | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | STE20 | YHL007C | Cdc42p-activated signal transducing kinase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | STU1 | YBL034C | Microtubule plus-end-tracking non-motor protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | SSB2 | YNL209W | Cytoplasmic ATPase that is a ribosome-associated molecular chaperone | physical | 1 | 1 | 1 | Co-purification | 
            
                | EAF7 | YNL136W | Subunit of the NuA4 histone acetyltransferase complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | HCM1 | YCR065W | Forkhead transcription factor | genetic | 1 | 1 | 1 | Phenotypic Enhancement | 
            
                | HRQ1 | YDR291W | 3'-5' DNA helicase of the conserved RecQ family | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | SCC4 | YER147C | Subunit of cohesin loading factor (Scc2p-Scc4p) | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MSS18 | YPR134W | Nuclear encoded protein needed for splicing of mitochondrial intron | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | GSH1 | YJL101C | Gamma glutamylcysteine synthetase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | YCK1 | YHR135C | Palmitoylated plasma membrane-bound casein kinase I (CK1) isoform | physical | 1 | 1 | 1 | Biochemical Activity | 
            
                | UBI4 | YLL039C | Ubiquitin | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | YRR1 | YOR162C | Zn2-Cys6 zinc-finger transcription factor | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | UPC2 | YDR213W | Sterol regulatory element binding protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | VPS52 | YDR484W | Component of the GARP (Golgi-associated retrograde protein) complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | TPK3 | YKL166C | cAMP-dependent protein kinase catalytic subunit | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | UBC9 | YDL064W | SUMO-conjugating enzyme involved in the Smt3p conjugation pathway | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | UBP3 | YER151C | Ubiquitin-specific protease that cleaves Ub-protein fusions | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | VPS53 | YJL029C | Component of the GARP (Golgi-associated retrograde protein) complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | YML054C-A | YML054C-A | Putative protein of unknown function | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | TUB4 | YLR212C | Gamma-tubulin | genetic | 1 | 1 | 1 | Synthetic Growth Defect | 
            
                | QCR8 | YJL166W | Subunit 8 of ubiquinol cytochrome-c reductase (Complex III) | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | RPL14A | YKL006W | Ribosomal 60S subunit protein L14A | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | SFB3 | YHR098C | Component of the Sec23p-Sfb3p heterodimer of the COPII vesicle coat | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | COX20 | YDR231C | Mitochondrial inner membrane protein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | CRS5 | YOR031W | Copper-binding metallothionein | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | MRPL50 | YNR022C | Mitochondrial ribosomal protein of the large subunit | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | CMC1 | YKL137W | Copper-binding protein of the mitochondrial intermembrane space | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | CRD1 | YDL142C | Cardiolipin synthase | genetic | 1 | 1 | 1 | Synthetic Lethality | 
            
                | ATX2 | YOR079C | Golgi membrane protein involved in manganese homeostasis | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PET8 | YNL003C | S-adenosylmethionine transporter of the mitochondrial inner membrane | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PCD1 | YLR151C | 8-oxo-dGTP diphosphatase | genetic | 1 | 1 | 1 | Negative Genetic |