| APE1 | YKL103C | Vacuolar aminopeptidase yscI | physical | 21 | 6 | 16 | Affinity Capture-MS, Two-hybrid, Two-hybrid, Affinity Capture-Western, Affinity Capture-Western, Reconstituted Complex, Two-hybrid, Two-hybrid, Affinity Capture-Western, Affinity Capture-Western, Two-hybrid, Two-hybrid, Co-localization, Affinity Capture-Western, Reconstituted Complex, Affinity Capture-MS, Reconstituted Complex, Co-crystal Structure, Reconstituted Complex, Reconstituted Complex, Reconstituted Complex | 
            
                | ATG8 | YBL078C | Ub-like protein | physical | 15 | 6 | 11 | Affinity Capture-Western, Protein-peptide, Two-hybrid, Reconstituted Complex, Two-hybrid, Affinity Capture-Western, Reconstituted Complex, Two-hybrid, Co-crystal Structure, Reconstituted Complex, Reconstituted Complex, Reconstituted Complex, Two-hybrid, Affinity Capture-MS, Affinity Capture-Western | 
            
                | ATG11 | YPR049C | Adapter protein for pexophagy and the Cvt targeting pathway | physical | 9 | 3 | 7 | Affinity Capture-Western, Two-hybrid, Two-hybrid, Affinity Capture-Western, Two-hybrid, Affinity Capture-Western, Affinity Capture-Western, Reconstituted Complex, Reconstituted Complex | 
            
                | AMS1 | YGL156W | Vacuolar alpha mannosidase | physical | 6 | 3 | 5 | Affinity Capture-Western, Two-hybrid, Affinity Capture-Western, Affinity Capture-Western, Two-hybrid, Reconstituted Complex | 
            
                | FKH1 | YIL131C | Forkhead family transcription factor | regulation | 4 | 3 | 4 | chromatin immunoprecipitation-chip evidence, chromatin immunoprecipitation-chip evidence, chromatin immunoprecipitation- exonuclease evidence, ChEC-Seq experiments | 
            
                | ATG1 | YGL180W | Protein serine/threonine kinase | physical | 4 | 3 | 3 | Affinity Capture-MS, Affinity Capture-Western, Biochemical Activity, Biochemical Activity | 
            
                | HRR25 | YPL204W | Conserved casein kinase, monopolin subunit | physical | 4 | 3 | 3 | Affinity Capture-MS, Biochemical Activity, Affinity Capture-Western, Biochemical Activity | 
            
                | APE4 | YHR113W | Cytoplasmic aspartyl aminopeptidase with possible vacuole function | physical | 4 | 2 | 3 | Two-hybrid, Two-hybrid, Affinity Capture-Western, Two-hybrid | 
            
                | ATG5 | YPL149W | Conserved protein involved in autophagy and the Cvt pathway | physical | 3 | 2 | 1 | Reconstituted Complex, Reconstituted Complex, Affinity Capture-Western | 
            
                | FKH2 | YNL068C | Forkhead family transcription factor | regulation | 2 | 2 | 2 | chromatin immunoprecipitation-chip evidence, ChEC-Seq experiments | 
            
                | ATG12 | YBR217W | Ubiquitin-like modifier involved in autophagy and the Cvt pathway | physical | 2 | 2 | 2 | Reconstituted Complex, Affinity Capture-MS | 
            
                | KIN1 | YDR122W | S/T protein kinase | physical | 2 | 2 | 2 | Two-hybrid, Affinity Capture-MS | 
            
                | KIN2 | YLR096W | S/T protein kinase | physical | 2 | 2 | 2 | Biochemical Activity, Reconstituted Complex | 
            
                | ATG19 | YOL082W | Receptor protein for the cytoplasm-to-vacuole targeting (Cvt) pathway | physical | 2 | 2 | 2 | Affinity Capture-MS, Reconstituted Complex | 
            
                | TFB1 | YDR311W | Subunit of TFIIH and nucleotide excision repair factor 3 complexes | physical | 2 | 1 | 2 | Two-hybrid, Two-hybrid | 
            
                | ATG16 | YMR159C | Conserved protein involved in autophagy | physical | 2 | 2 | 1 | Reconstituted Complex, PCA | 
            
                | UBP3 | YER151C | Ubiquitin-specific protease that cleaves Ub-protein fusions | physical | 2 | 2 | 1 | Two-hybrid, Reconstituted Complex | 
            
                | SFP1 | YLR403W | Regulates transcription of ribosomal protein and biogenesis genes | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | STE12 | YHR084W | Transcription factor that is activated by a MAPK signaling cascade | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip 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 | chromatin immunoprecipitation-chip evidence | 
            
                | REB1 | YBR049C | RNA polymerase I enhancer binding protein | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | SUA7 | YPR086W | Transcription factor TFIIB | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | ZAP1 | YJL056C | Zinc-regulated transcription factor | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | CST6 | YIL036W | Basic leucine zipper (bZIP) transcription factor from ATF/CREB family | regulation | 1 | 1 | 1 | DNA to cDNA expression microarray evidence | 
            
                | PHO2 | YDL106C | Homeobox transcription factor | regulation | 1 | 1 | 1 | chromatin immunoprecipitation-chip evidence | 
            
                | NAB3 | YPL190C | RNA-binding protein, subunit of Nrd1 complex (Nrd1p-Nab3p-Sen1p) | regulation | 1 | 1 | 1 | quantitative reverse transcription polymerase chain reaction evidence | 
            
                | HRR25 | YPL204W | Conserved casein kinase, monopolin subunit | regulation | 1 | 1 | 1 | protein kinase assay evidence | 
            
                | ATG1 | YGL180W | Protein serine/threonine kinase | regulation | 1 | 1 | 1 | protein kinase assay evidence | 
            
                | TRS33 | YOR115C | Core component of TRAPP complexes I, II and IV | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | UME6 | YDR207C | Rpd3L histone deacetylase complex subunit | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | SOG2 | YOR353C | Key component of the RAM signaling network | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | IRE1 | YHR079C | Serine-threonine kinase and endoribonuclease | physical | 1 | 1 | 1 | Biochemical Activity | 
            
                | PTK2 | YJR059W | Serine/threonine protein kinase | physical | 1 | 1 | 1 | Biochemical Activity | 
            
                | TOS3 | YGL179C | Protein kinase | physical | 1 | 1 | 1 | Biochemical Activity | 
            
                | SRP1 | YNL189W | Karyopherin alpha homolog | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | GLR1 | YPL091W | Cytosolic and mitochondrial glutathione oxidoreductase | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | MXR2 | YCL033C | Methionine-R-sulfoxide reductase | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | PAM16 | YJL104W | Subunit of the import motor (PAM complex) | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | PHA2 | YNL316C | Prephenate dehydratase | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | SMC5 | YOL034W | Subunit of the SMC5-SMC6 complex | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | ISU1 | YPL135W | Conserved protein of the mitochondrial matrix | physical | 1 | 1 | 1 | Two-hybrid | 
            
                | NAB2 | YGL122C | Nuclear polyadenylated RNA-binding protein | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | DUN1 | YDL101C | Cell-cycle checkpoint S/T protein kinase | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | RAD53 | YPL153C | DNA damage response kinase | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | YPK2 | YMR104C | AGC-type S/T protein kinase | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | PHO85 | YPL031C | Cyclin-dependent kinase | physical | 1 | 1 | 1 | Biochemical Activity | 
            
                | CTK1 | YKL139W | Catalytic (alpha) subunit of C-terminal domain kinase I (CTDK-I) | physical | 1 | 1 | 1 | Reconstituted Complex | 
            
                | FRK1 | YPL141C | Protein kinase of unknown cellular role | physical | 1 | 1 | 1 | Reconstituted Complex | 
            
                | MEK1 | YOR351C | Meiosis-specific serine/threonine protein kinase | physical | 1 | 1 | 1 | Reconstituted Complex | 
            
                | MKK1 | YOR231W | MAPKK involved in the protein kinase C signaling pathway | physical | 1 | 1 | 1 | Reconstituted Complex | 
            
                | PKH2 | YOL100W | Serine/threonine protein kinase | physical | 1 | 1 | 1 | Reconstituted Complex | 
            
                | PKH3 | YDR466W | Protein kinase with similarity to mammalian PDK1 and yeast Pkh1p/Phk2p | physical | 1 | 1 | 1 | Reconstituted Complex | 
            
                | YAR010C | YAR010C | Retrotransposon TYA Gag gene co-transcribed with TYB Pol | physical | 1 | 1 | 1 | Affinity Capture-Western | 
            
                | CRM1 | YGR218W | Nuclear export factor, exportin | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | EFT2 | YDR385W | Elongation factor 2 (EF-2), also encoded by EFT1 | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | SSA2 | YLL024C | HSP70 family ATP-binding protein | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | SSB1 | YDL229W | Cytoplasmic ATPase that is a ribosome-associated molecular chaperone | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | HSC82 | YMR186W | Cytoplasmic chaperone of the Hsp90 family | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | CDC19 | YAL038W | Pyruvate kinase | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | PAB1 | YER165W | Poly(A) binding protein | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | SSC1 | YJR045C | Hsp70 family ATPase | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | PFK2 | YMR205C | Beta subunit of heterooctameric phosphofructokinase | physical | 1 | 1 | 1 | Affinity Capture-MS | 
            
                | DHH1 | YDL160C | Cytoplasmic DEAD-box helicase and mRNA decapping activator | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | CCR4 | YAL021C | Component of the CCR4-NOT transcriptional complex | physical | 1 | 1 | 1 | Affinity Capture-RNA | 
            
                | FUS2 | YMR232W | Cell fusion regulator | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | JID1 | YPR061C | Probable Hsp40p co-chaperone | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | ATG34 | YOL083W | Receptor protein involved in selective autophagy during starvation | genetic | 1 | 1 | 1 | Phenotypic Enhancement | 
            
                | PNG1 | YPL096W | Conserved peptide N-glycanase | genetic | 1 | 1 | 1 | Phenotypic Suppression | 
            
                | TAF1 | YGR274C | TFIID subunit, involved in RNA pol II transcription initiation | genetic | 1 | 1 | 1 | Synthetic Lethality | 
            
                | ATG21 | YPL100W | Phosphoinositide binding protein | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | ATG29 | YPL166W | Autophagy-specific protein | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | ATG32 | YIL146C | Mitochondrial outer membrane protein required to initiate mitophagy | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | ATG33 | YLR356W | Mitochondrial mitophagy-specific protein | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | CCZ1 | YBR131W | Subunit of a heterodimeric guanine nucleotide exchange factor (GEF) | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | PHO80 | YOL001W | Cyclin | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | REG1 | YDR028C | Regulatory subunit of type 1 protein phosphatase Glc7p | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | SNF1 | YDR477W | AMP-activated S/T protein kinase | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | SNX4 | YJL036W | Sorting nexin | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | TEP1 | YNL128W | PTEN homolog with no demonstrated inositol lipid phosphatase activity | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | TLG2 | YOL018C | Syntaxin-like t-SNARE | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | VPS30 | YPL120W | Subunit of phosphatidylinositol (PtdIns) 3-kinase complexes I and II | genetic | 1 | 1 | 1 | Positive Genetic | 
            
                | TPK3 | YKL166C | cAMP-dependent protein kinase catalytic subunit | genetic | 1 | 1 | 1 | Phenotypic Suppression | 
            
                | ROF1 | YHR177W | Putative transcription factor containing a WOPR domain | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PEX19 | YDL065C | Chaperone and import receptor for newly-synthesized class I PMPs | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | EMP65 | YER140W | Integral membrane protein of the ER | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | STF2 | YGR008C | Protein involved in resistance to desiccation stress | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | SNF6 | YHL025W | Subunit of the SWI/SNF chromatin remodeling complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | YRA2 | YKL214C | Member of the REF (RNA and export factor binding proteins) family | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | HCR1 | YLR192C | eIF3j component of translation initiation factor 3 (eIF3) | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | COA4 | YLR218C | Twin Cx(9)C protein involved in cytochrome c oxidase organization | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | BUL2 | YML111W | Alpha-arrestin, component of the Rsp5p E3-ubiquitin ligase complex | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | COX7 | YMR256C | Subunit VII of cytochrome c oxidase (Complex IV) | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | SCS7 | YMR272C | Sphingolipid alpha-hydroxylase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | VAM3 | YOR106W | Syntaxin-like vacuolar t-SNARE | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | PMA2 | YPL036W | Plasma membrane H+-ATPase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | RPL21B | YPL079W | Ribosomal 60S subunit protein L21B | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | YPR089W | YPR089W | Protein of unknown function | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | EEB1 | YPL095C | Acyl-coenzymeA:ethanol O-acyltransferase | genetic | 1 | 1 | 1 | Negative Genetic | 
            
                | ATG10 | YLL042C | Conserved E2-like conjugating enzyme | genetic | 1 | 1 | 1 | Positive Genetic |