S1 Table

Dal80 Prom (1269) Peak Calling YAL002W VPS8 Vacuolar Protein Sorting YAL003W EFB1 Elongation Factor Beta YAL005C SSA1 Stress-Seventy subfamily A YAL028W FRT2 Functionally Related to TCP1 YAL029C MYO4 MYOsin YAL038W CDC19 Cell Division Cycle YAL039C CYC3 CYtochrome C YAL051W OAF1 Oleate-Activated transcription Factor YAL053W FLC2 FLavin Carrier YAL059W ECM1 ExtraCellular Mutant YAL060W BDH1 Butanediol DeHydrogenase YAL062W GDH3 Glutamate DeHydrogenase YAR035W YAT1 YBL002W HTB2 Histone h Two B YBL003C HTA2 Histone h Two A YBL005W PDR3 Pleiotropic Drug Resistance YBL011W SCT1 Suppressor of Choline-Transport mutants YBL014C RRN6 Regulation of RNA polymerase I YBL016W FUS3 cell FUSion YBL026W LSM2 Like SM YBL027W RPL19B Ribosomal Protein of the Large subunit YBL028C YBL029C-A YBL029W YBL030C PET9 PETite YBL032W HEK2 HEterogeneous nuclear rnp K-like YBL033C RIB1 RIBoflavin biosynthesis YBL038W MRPL16 Mitochondrial Ribosomal Protein, Large subunit YBL039C URA7 URAcil requiring YBL041W PRE7 PRoteinase yscE YBL042C FUI1 5-FlUorourIdine resistance YBL044W YBL055C YBL064C PRX1 PeroxiRedoXin YBL071C-B YBL071W-A KTI11 Kluveromyces lactis Toxin Insensitive YBL072C RPS8A Ribosomal Protein of the Small subunit YBL074C AAR2 A1-Alpha2 Repression YBL075C SSA3 Stress-Seventy subfamily A YBL085W BOI1 Bem1 (One) Interacting protein YBL087C RPL23A Ribosomal Protein of the Large subunit YBL092W RPL32 Ribosomal Protein of the Large subunit YBL093C ROX3 Regulation by OXygen YBL101C ECM21 ExtraCellular Mutant YBR006W UGA2 Utilization of GAba YBR007C DSF2 Deletion Suppressor of mptFive/pufFive mutation YBR009C HHF1 Histone H Four YBR010W HHT1 Histone H Three YBR016W

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YBR019C GAL10 GALactose metabolism YBR021W FUR4 5-FlUoRouridine sensitivity YBR025C OLA1 Obg-Like ATPase YBR037C SCO1 Suppressor of Cytochrome Oxidase deficiency YBR038W CHS2 CHitin YBR042C CST26 STability YBR043C QDR3 QuiniDine Resistance YBR046C ZTA1 ZeTA-crystallin YBR048W RPS11B Ribosomal Protein of the Small subunit YBR049C REB1 RNA polymerase I Enhancer Binding protein YBR056W YBR067C TIP1 Temperature shock-Inducible Protein YBR070C ALG14 Asparagine Linked Glycosylation YBR071W YBR077C SLM4 Synthetic Lethal with Mss4 YBR078W ECM33 ExtraCellular Mutant YBR082C UBC4 UBiquitin-Conjugating YBR083W TEC1 Transposon Enhancement Control YBR084C-A RPL19A Ribosomal Protein of the Large subunit YBR084W MIS1 MItochondrial C1-tetrahydrofolate Synthase YBR085C-A YBR085W AAC3 ADP/ATP Carrier YBR088C POL30 POLymerase YBR089C-A NHP6B Non-Histone Protein YBR101C FES1 Factor Exchange for Ssa1p YBR104W YMC2 Yeast Mitochondrial Carrier YBR105C VID24 Vacuolar Import and Degradation YBR106W PHO88 PHOsphate metabolism YBR112C CYC8 CYtochrome C YBR114W RAD16 RADiation sensitive YBR115C LYS2 LYSine requiring YBR118W TEF2 Translation Elongation Factor YBR119W MUD1 Mutant U1 Die YBR127C VMA2 Vacuolar Membrane Atpase YBR133C HSL7 Histone Synthetic Lethal YBR135W CKS1 Cdc28 Kinase Subunit YBR137W YBR145W ADH5 Alcohol DeHydrogenase YBR147W RTC2 Restriction of Telomere Capping YBR150C TBS1 ThiaBendazole Sensitive YBR151W APD1 Actin Patches Distal YBR153W RIB7 RIBoflavin biosynthesis YBR161W CSH1 CSG1/SUR1 Homolog YBR162W-A YSY6 YBR163W EXO5 EXOnuclease V YBR177C EHT1 Ethanol Hexanoyl YBR179C FZO1 FuZzy Onions homolog YBR180W DTR1 DiTyRosine YBR181C RPS6B Ribosomal Protein of the Small subunit

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YBR182C-A YBR183W YPC1 Yeast Phyto-Ceramidase YBR187W GDT1 Gcr1 Dependent Translation factor YBR188C NTC20 Prp19p (NineTeen)-associated Complex YBR189W RPS9B Ribosomal Protein of the Small subunit YBR191W RPL21A Ribosomal Protein of the Large subunit YBR196C PGI1 PhosphoGlucoIsomerase YBR196C-A YBR201C-A YBR202W MCM7 MiniChromosome Maintenance YBR208C DUR1,2 Degradation of URea YBR218C PYC2 PYruvate Carboxylase YBR222C PCS60 Peroxisomal CoA-dependent Synthetase YBR230C OM14 Outer Membrane Protein of 14 kDa YBR230W-A YBR238C YBR248C HIS7 HIStidine requiring YBR291C CTP1 Citrate Transport Protein YBR297W MAL33 MALtose YCL009C ILV6 IsoLeucine Valine YCL010C SGF29 SaGa associated Factor YCL018W LEU2 LEUcine biosynthesis YCL024W KCC4 YCL030C HIS4 HIStidine requiring YCL031C RRP7 Ribosomal RNA Processing YCL037C SRO9 Suppressor of rho3 YCL040W GLK1 GLucoKinase YCL043C PDI1 Protein Disulfide YCL050C APA1 AP4A YCL064C CHA1 Catabolism of Hydroxy Amino acids YCR005C CIT2 CITrate synthase YCR012W PGK1 3-PhosphoGlycerate Kinase YCR024C-A PMP1 Plasma Membrane Proteolipid YCR031C RPS14A Ribosomal Protein of the Small subunit YCR047C BUD23 BUD site selection YCR048W ARE1 Acyl-coenzyme A: cholesterol acyl transferase-Related YCR061W YCR063W BUD31 BUD site selection YCR067C SED4 Suppressor of Erd2 Deletion YCR073C SSK22 Suppressor of Sensor Kinase YCR073W-A SOL2 Suppressor Of Los1-1 YDL022W GPD1 Glycerol-3-Phosphate Dehydrogenase YDL048C STP4 protein with similarity to Stp1p YDL049C KNH1 Kre9(Nine) Homolog YDL055C PSA1 YDL060W TSR1 Twenty S rRNA accumulation YDL061C RPS29B Ribosomal Protein of the Small subunit YDL066W IDP1 Isocitrate Dehydrogenase, NADP-specific YDL067C COX9 Cytochrome c OXidase

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YDL070W BDF2 BromoDomain Factor YDL072C YET3 Yeast Endoplasmic reticulum Transmembrane protein YDL075W RPL31A Ribosomal Protein of the Large subunit YDL076C RXT3 YDL082W RPL13A Ribosomal Protein of the Large subunit YDL083C RPS16B Ribosomal Protein of the Small subunit YDL085C-A YDL095W PMT1 Protein O- YDL111C RRP42 Ribosomal RNA Processing YDL124W YDL125C HNT1 Histidine triad NucleoTide-binding YDL128W VCX1 VaCuolar H+/Ca2+ eXchanger YDL129W YDL130W RPP1B Ribosomal Protein P1 Beta YDL130W-A STF1 STabilizing Factor YDL131W LYS21 LYSine YDL133C-A RPL41B Ribosomal Protein of the Large subunit YDL133W SRF1 Spo14 Regulatory Factor YDL136W RPL35B Ribosomal Protein of the Large subunit YDL137W ARF2 ADP-Ribosylation Factor YDL138W RGT2 Restores Glucose Transport YDL155W CLB3 CycLin B YDL170W UGA3 Utilization of GAba YDL171C GLT1 GLuTamate synthase YDL174C DLD1 D-Lactate Dehydrogenase YDL180W YDL181W INH1 INHibitor (of F1F0-ATPase) YDL182W LYS20 LYSine requiring YDL183C YDL184C RPL41A Ribosomal Protein of the Large subunit YDL191W RPL35A Ribosomal Protein of the Large subunit YDL198C GGC1 GDP/GTP Carrier YDL199C YDL210W UGA4 Utilization of GAba YDL215C GDH2 Glutamate DeHydrogenase YDL229W SSB1 Stress-Seventy subfamily B YDL230W PTP1 Protein Tyrosine Phosphatase YDL231C BRE4 BREfeldin A sensitivity YDL236W PHO13 PHOsphate metabolism YDR003W RCR2 Resistance to Congo Red YDR006C SOK1 Suppressor Of Kinase YDR022C ATG31 AuTophaGy related YDR025W RPS11A Ribosomal Protein of the Small subunit YDR034C LYS14 LYSine requiring YDR034W-B YDR035W ARO3 AROmatic amino acid requiring YDR036C EHD3 YDR037W KRS1 Lysyl (K) tRNA Synthetase YDR041W RSM10 Ribosomal Small subunit of Mitochondria

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YDR050C TPI1 Triose-Phosphate Isomerase YDR058C TGL2 TriacylGlycerol Lipase YDR061W YDR064W RPS13 Ribosomal Protein of the Small subunit YDR072C IPT1 InositolPhosphoTransferase YDR073W SNF11 Sucrose NonFermenting YDR077W SED1 Suppression of Exponential Defect YDR089W VTC5 Vacuole Transporter Chaperone YDR090C YDR099W BMH2 Brain Modulosignalin Homolog YDR119W VBA4 Vacuolar Basic Amino acid transporter YDR123C INO2 INOsitol requiring YDR127W ARO1 AROmatic amino acid requiring YDR147W EKI1 Ethanolamine KInase YDR150W NUM1 NUclear Migration YDR151C CTH1 Cysteine-Three-Histidine YDR152W GIR2 Genetically Interacts with Ribosomal YDR153C ENT5 Epsin N-Terminal homology YDR155C CPR1 Cyclosporin A-sensitive Proline Rotamase YDR156W RPA14 RNA Polymerase A YDR158W HOM2 HOMoserine requiring YDR171W HSP42 Heat Shock Protein YDR173C ARG82 ARGinine requiring YDR174W HMO1 High MObility group (HMG) family YDR186C SND1 Srp-iNDependent targeting YDR188W CCT6 Chaperonin Containing TCP-1 YDR207C UME6 Unscheduled Meiotic gene Expression YDR208W MSS4 Multicopy Suppressor of Stt4 mutation YDR210W YDR211W GCD6 General Control Derepressed YDR214W AHA1 Activator of Heat shock protein 90 ATPase YDR224C HTB1 Histone h Two B YDR225W HTA1 Histone h Two A YDR226W ADK1 ADenylate Kinase YDR231C COX20 Cytochrome c OXidase YDR232W HEM1 HEMe biosynthesis YDR233C RTN1 ReTiculoN-like YDR234W LYS4 LYSine requiring YDR242W AMD2 AMiDase YDR244W PEX5 PEroXin YDR258C HSP78 Heat Shock Protein YDR262W YDR270W CCC2 Cross-Complements Ca(2+) phenotype of csg1 YDR275W BSC2 Bypass of Stop Codon YDR276C PMP3 Plasma Membrane Proteolipid YDR297W SUR2 SUppressor of Rvs161 and rvs167 mutations YDR309C GIC2 GTPase Interactive Component YDR313C PIB1 PhosphatidylInositol(3)-phosphate Binding YDR341C

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YDR345C HXT3 HeXose Transporter YDR347W MRP1 Mitochondrial Ribosomal Protein YDR354W TRP4 TRyPtophan YDR357C CNL1 CNo-Like YDR358W GGA1 Golgi-localized, Gamma-adaptin ear homology, Arf-binding protein YDR359C EAF1 Esa1p-Associated Factor YDR362C TFC6 Transcription Factor C YDR363W ESC2 Establishment of Silent Chromatin YDR380W ARO10 AROmatic amino acid requiring YDR381W YRA1 Yeast RNA Annealing protein YDR384C ATO3 Ammonia (Ammonium) Transport Outward YDR385W EFT2 Elongation Factor Two YDR390C UBA2 UBiquitin Activating YDR399W HPT1 Hypoxanthine guanine PhosphoribosylTransferase YDR441C APT2 Adenine PhosphoribosylTransferase YDR447C RPS17B Ribosomal Protein of the Small subunit YDR448W ADA2 transcriptional ADAptor YDR450W RPS18A Ribosomal Protein of the Small subunit YDR451C YHP1 Yeast Homeo-Protein YDR470C UGO1 UGO (Japanese for fusion) YDR471W RPL27B Ribosomal Protein of the Large subunit YDR481C PHO8 PHOsphate metabolism YDR487C RIB3 RIBoflavin biosynthesis YDR490C PKH1 Pkb-activating Kinase Homolog YDR492W IZH1 Implicated in Zinc Homeostasis YDR496C PUF6 PUmilio-homology domain Family YDR497C ITR1 myo-Inositol TRansporter YDR499W LCD1 Lethal, Checkpoint-defective, DNA damage sensitive YDR500C RPL37B Ribosomal Protein of the Large subunit YDR501W PLM2 PLasmid Maintenance YDR502C SAM2 S-AdenosylMethionine requiring YDR507C GIN4 Growth Inhibitory YDR510W SMT3 Suppressor of Mif Two YDR516C EMI2 Early Meiotic Induction YDR524C AGE1 Arf Gap with Effector function(s) YDR524C-B YDR524W-C YDR525W-A SNA2 Sensitivity to NA+ YDR527W RBA50 RNA polymerase II (B) Associated protein YDR529C QCR7 ubiQuinol-cytochrome C YDR530C APA2 AP4A phosphorylase YDR531W CAB1 Coenzyme A Biosynthesis YDR533C HSP31 Heat-Shock Protein YEL007W MIT1 Muc1 expressed Independent of TEC1 YEL017C-A PMP2 Plasma Membrane Proteolipid YEL017W GTT3 GlutaThione Transferase YEL021W URA3 URAcil requiring YEL024W RIP1 Rieske Iron-sulfur Protein YEL026W SNU13 Small NUclear ribonucleoprotein associated

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YEL027W VMA3 Vacuolar Membrane Atpase YEL032W MCM3 MiniChromosome Maintenance YEL034W HYP2 HYPusine-containing protein YEL036C ANP1 ANP and osmotic sensitive YEL040W UTR2 Unidentified TRanscript YEL044W IES6 Ino Eighty Subunit YEL046C GLY1 GLYcine requiring YEL054C RPL12A Ribosomal Protein of the Large subunit YEL055C POL5 POLymerase YEL058W PCM1 PhosphoaCetylglucosamine Mutase YEL059C-A SOM1 SOrting Mitochondrial YEL060C PRB1 PRoteinase B YEL063C CAN1 CANavanine resistance YEL065W SIT1 Siderophore Iron Transport YEL071W DLD3 D-Lactate Dehydrogenase YEL072W RMD6 Required for Meiotic nuclear Division YER001W MNN1 MaNNosyltransferase YER019C-A SBH2 Sec61 beta homolog 2 YER019W ISC1 Inositol phosphoSphingolipid phospholipase C YER020W GPA2 G Protein Alpha subunit YER024W YAT2 YER028C MIG3 Multicopy Inhibitor of Growth YER031C YPT31 Yeast Protein Two YER033C ZRG8 Zinc Regulated Gene YER034W YER035W EDC2 Enhancer of mRNA DeCapping YER036C ARB1 ATP-binding cassette protein involved in Ribosome Biogenesis YER037W PHM8 PHosphate Metabolism YER043C SAH1 S-Adenosyl-l-Homocysteine YER044C ERG28 ERGosterol biosynthesis YER046W SPO73 SPOrulation YER052C HOM3 HOMoserine requiring YER055C HIS1 HIStidine YER056C FCY2 FluoroCYtosine resistance YER056C-A RPL34A Ribosomal Protein of the Large subunit YER068W MOT2 Modulator Of Transcription YER069W ARG5,6 ARGinine requiring YER073W ALD5 ALdehyde Dehydrogenase YER074W RPS24A Ribosomal Protein of the Small subunit YER075C PTP3 Protein Tyrosine Phosphatase YER081W SER3 SERine requiring YER085C YER086W ILV1 IsoLeucine-plus-Valine requiring YER088C DOT6 Disruptor Of Telomeric silencing YER091C MET6 METhionine requiring YER092W IES5 Ino Eighty Subunit YER094C PUP3 PUtative Proteasome subunit YER095W RAD51 RADiation sensitive YER102W RPS8B Ribosomal Protein of the Small subunit

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YER103W SSA4 Stress-Seventy subfamily A YER116C SLX8 Synthetic Lethal of unknown (X) function YER117W RPL23B Ribosomal Protein of the Large subunit YER130C COM2 Cousin of Msn2 YER131W RPS26B Ribosomal Protein of the Small subunit YER136W GDI1 GDP Dissociation Inhibitor YER137C YER145C FTR1 Fe TRansporter YER146W LSM5 Like SM YER150W SPI1 Stationary Phase Induced YER155C BEM2 Bud EMergence YER159C BUR6 Bypass UAS Requirement YER168C CCA1 tRNA CCA-pyrophosphorylase YER174C GRX4 GlutaRedoXin YER175C TMT1 Trans-aconitate MethylTransferase YER177W BMH1 Brain Modulosignalin Homolog YER178W PDA1 Pyruvate Dehydrogenase Alpha YER180C-A SLO1 Scoco-Like Orf YER185W PUG1 Protoporphyrin Uptake Gene YFL016C MDJ1 Mitochondrial DnaJ YFL021W GAT1 YFL022C FRS2 phenylalanyl (F)-tRNA Synthetase YFL023W BUD27 BUD site selection YFL024C EPL1 Enhancer of Polycomb Like YFL030W AGX1 Alanine:Glyoxylate aminotrans(X)ferase YFL031W HAC1 Homologous to Atf/Creb1 YFL037W TUB2 TUBulin YFL038C YPT1 Yeast Protein Two YFL039C ACT1 ACTin YFL054C AQY3 AQuaporin from Yeast YFR006W YFR009W GCN20 General Control Nonderepressible YFR025C HIS2 HIStidine requiring YFR029W PTR3 Peptide TRansport YFR030W MET10 METhionine requiring YFR031C-A RPL2A Ribosomal Protein of the Large subunit YFR032C-A RPL29 Ribosomal Protein of the Large subunit YFR033C QCR6 ubiQuinol-cytochrome C oxidoReductase YFR034C PHO4 PHOsphate metabolism YFR035C YFR036W CDC26 Cell Division Cycle YFR039C OSW7 Outer Spore Wall YFR055W IRC7 Increased Recombination Centers YGL001C ERG26 ERGosterol biosynthesis YGL007C-A YGL009C LEU1 LEUcine biosynthesis YGL012W ERG4 ERGosterol biosynthesis YGL013C PDR1 Pleiotropic Drug Resistance YGL029W CGR1 Coiled-coil Growth-Regulated

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YGL030W RPL30 Ribosomal Protein of the Large subunit YGL031C RPL24A Ribosomal Protein of the Large subunit YGL035C MIG1 Multicopy Inhibitor of GAL gene expression YGL037C PNC1 Pyrazinamidase and NiCotinamidase YGL038C OCH1 Outer CHain elongation YGL040C HEM2 HEMe biosynthesis YGL050W TYW3 Trna-YW synthesizing protein YGL056C SDS23 homolog of S. pombe SDS23 YGL062W PYC1 PYruvate Carboxylase YGL076C RPL7A Ribosomal Protein of the Large subunit YGL077C HNM1 Hyper-resistance to Nitrogen Mustard YGL083W SCY1 YGL096W TOS8 Target Of Sbf YGL101W YGL103W RPL28 Ribosomal Protein of the Large subunit YGL115W SNF4 Sucrose NonFermenting YGL117W YGL123W RPS2 Ribosomal Protein of the Small subunit YGL125W MET13 METhionine requiring YGL134W PCL10 Pho85 CycLin YGL135W RPL1B Ribosomal Protein of the Large subunit YGL145W TIP20 SEC20 (Twenty) Interacting Protein YGL146C RRT6 Regulator of rDNA Transcription YGL147C RPL9A Ribosomal Protein of the Large subunit YGL148W ARO2 AROmatic amino acid requiring YGL150C INO80 INOsitol requiring YGL166W CUP2 YGL184C STR3 Sulfur TRansfer YGL186C TPN1 Transport of PyridoxiNe YGL187C COX4 Cytochrome c OXidase YGL188C-A YGL189C RPS26A Ribosomal Protein of the Small subunit YGL196W DSD1 YGL197W MDS3 Mck1 Dosage Suppressor YGL202W ARO8 AROmatic amino acid requiring YGL206C CHC1 Clathrin Heavy Chain YGL209W MIG2 Multicopy Inhibitor of GAL gene expression YGL219C MDM34 Mitochondrial Distribution and Morphology YGL225W VRG4 Vandate Resistance Glycosylation YGL228W SHE10 Sensitivity to High Expression YGL236C MTO1 Mitochondrial Translation Optimization YGL253W HXK2 HeXoKinase YGR019W UGA1 Utilization of GAba YGR020C VMA7 Vacuolar Membrane Atpase YGR021W YGR027C RPS25A Ribosomal Protein of the Small subunit YGR031C-A NAG1 Nested Antisense Gene YGR031W IMO32 Intermediate cleaved by Mitochondrial Octapeptidyl aminopeptidase YGR033C TIM21 of the Inner Mitochondrial membrane

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YGR034W RPL26B Ribosomal Protein of the Large subunit YGR035C YGR037C ACB1 Acyl-CoA-Binding YGR044C RME1 Regulator of MEiosis YGR047C TFC4 Transcription Factor class C YGR048W UFD1 Ubiquitin Fusion Degradation protein YGR060W ERG25 ERGosterol biosynthesis YGR061C ADE6 ADEnine requiring YGR065C VHT1 Vitamin H Transporter YGR078C PAC10 Perish in the Absence of Cin8p YGR079W YGR085C RPL11B Ribosomal Protein of the Large subunit YGR086C PIL1 Phosphorylation Inhibited by Long chain bases YGR092W DBF2 DumbBell Former YGR106C VOA1 V0 Assembly protein YGR110W CLD1 CardioLipin-specific Deacylase YGR117C YGR118W RPS23A Ribosomal Protein of the Small subunit YGR120C COG2 Conserved Oligomeric Golgi complex YGR121C MEP1 YGR121W-A YGR122W YGR124W ASN2 ASparagiNe requiring YGR125W YGR126W YGR142W BTN2 BaTteN disease YGR146C-A YGR148C RPL24B Ribosomal Protein of the Large subunit YGR152C RSR1 RaS-Related YGR154C GTO1 Glutathione Transferase Omega-like YGR155W CYS4 CYStathionine beta-synthase YGR156W PTI1 PTa1p Interacting protein YGR157W CHO2 CHOline requiring YGR159C NSR1 YGR161C RTS3 YGR161W-C YGR162W TIF4631 Translation Initiation Factor YGR165W MRPS35 Mitochondrial Ribosomal Protein, Small subunit YGR169C-A LSO2 Late-annotated Small Open reading frame YGR170W PSD2 PhosphatidylSerine Decarboxylase YGR175C ERG1 ERGosterol biosynthesis YGR180C RNR4 RiboNucleotide Reductase YGR183C QCR9 ubiQuinol-cytochrome C oxidoReductase YGR191W HIP1 HIstidine Permease YGR192C TDH3 Triose-phosphate DeHydrogenase YGR197C SNG1 YGR198W YPP1 alpha-sYnuclein Protective Protein YGR202C PCT1 Phosphocholine CytidylylTransferase YGR203W YCH1 Yeast Cdc25 Homolog

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Dal80 Prom (1269) Peak Calling YGR204W ADE3 ADEnine requiring YGR210C YGR211W ZPR1 Zinc finger PRotein YGR214W RPS0A Ribosomal Protein of the Small subunit YGR221C TOS2 Target Of Sbf YGR223C HSV2 Homologous with SVP1 YGR238C KEL2 KELch repeat YGR239C PEX21 PEroXin YGR243W MPC3 Mitochondrial Pyruvate Carrier YGR244C LSC2 of Succinyl-CoA YGR254W ENO1 ENOlase YGR255C COQ6 COenzyme Q YGR268C HUA1 YGR279C SCW4 Soluble Cell Wall protein YGR280C PXR1 PinX1-Related gene YHL001W RPL14B Ribosomal Protein of the Large subunit YHL004W MRP4 Mitochondrial Ribosomal Protein YHL006C SHU1 Suppressor of HU sensitivity YHL007C STE20 STErile YHL015W RPS20 Ribosomal Protein of the Small subunit YHL015W-A YHL016C DUR3 Degradation of URea YHL020C OPI1 OverProducer of Inositol YHL021C AIM17 Altered Inheritance rate of Mitochondria YHL023C NPR3 Nitrogen Permease Regulator YHL025W SNF6 Sucrose NonFermenting YHL026C YHL028W WSC4 cell Wall integrity and Stress response Component YHL029C OCA5 Oxidant-induced Cell-cycle Arrest YHL033C RPL8A Ribosomal Protein of the Large subunit YHL040C ARN1 AFT1 ReguloN YHR005C GPA1 G Protein Alpha subunit YHR005C-A TIM10 Translocase of the Inner Membrane YHR007C ERG11 ERGosterol biosynthesis YHR008C SOD2 SuperOxide Dismutase YHR010W RPL27A Ribosomal Protein of the Large subunit YHR015W MIP6 Mex67-Interacting Protein YHR018C ARG4 ARGinine requiring YHR019C DED81 Defines Essential Domain YHR020W YHR021C RPS27B Ribosomal Protein of the Small subunit YHR021W-A ECM12 ExtraCellular Mutant YHR023W MYO1 MYOsin YHR028C DAP2 Dipeptidyl AminoPeptidase YHR029C YHI9 YHR031C RRM3 rDNA Recombination Mutation YHR033W YHR037W PUT2 Proline UTilization YHR038W RRF1 Ribosome Recycling Factor

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YHR041C SRB2 Suppressor of RNA polymerase B YHR042W NCP1 NADP-Cytochrome P450 reductase YHR047C AAP1 Arginine/alanine AminoPeptidase YHR048W YHK8 YHR049W FSH1 Family of Serine YHR051W COX6 Cytochrome c OXidase YHR067W HTD2 Hydroxyacyl-Thioester Dehydratase YHR083W SAM35 Sorting and Assembly Machinery YHR094C HXT1 HeXose Transporter YHR097C YHR098C SFB3 Sed Five Binding YHR099W TRA1 similar to human TRRAP YHR128W FUR1 5-FluoroURidine resistant YHR137W ARO9 AROmatic amino acid requiring YHR141C RPL42B Ribosomal Protein of the Large subunit YHR144C DCD1 dCMP Deaminase YHR149C SKG6 Suppressor of lethality of Kex2 Gas1 double null mutant YHR150W PEX28 PEroXisome related YHR151C MTC6 Maintenance of Telomere Capping YHR152W SPO12 SPOrulation YHR162W MPC2 Mitochondrial Pyruvate Carrier YHR163W SOL3 Suppressor Of Los1-1 YHR174W ENO2 ENOlase YHR175W CTR2 Copper TRansport YHR179W OYE2 Old Yellow Enzyme YHR181W SVP26 Sed5 Vesicle Protein YHR183W GND1 6-phosphoGlucoNateDehydrogenase YHR193C EGD2 Enhancer of Gal4 DNA binding YHR194W MDM31 Mitochondrial Distribution and Morphology YHR195W NVJ1 Nucleus-Vacuole Junction YHR200W RPN10 Regulatory Particle Non-ATPase YHR203C RPS4B Ribosomal Protein of the Small subunit YHR208W BAT1 Branched-chain Amino acid Transaminase YIL009W FAA3 Fatty Acid Activation YIL014C-A YIL018W RPL2B Ribosomal Protein of the Large subunit YIL033C BCY1 Bypass of CYclic-AMP requirement YIL046W MET30 METhionine requiring YIL046W-A YIL047C SYG1 Suppressor of Yeast Gpa1 YIL050W PCL7 Pho85 CycLin YIL051C MMF1 Mitochondrial Matrix Factor YIL052C RPL34B Ribosomal Protein of the Large subunit YIL053W GPP1 Glycerol-3-Phosphate Phosphatase YIL055C YIL056W VHR1 VHt1 Regulator YIL061C SNP1 YIL069C RPS24B Ribosomal Protein of the Small subunit YIL074C SER33 SERine requiring

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YIL077C YIL094C LYS12 LYSine requiring YIL099W SGA1 Sporulation-specific GlycoAmylase YIL114C POR2 PORin YIL116W HIS5 HIStidine requiring YIL117C PRM5 Pheromone-Regulated Membrane protein YIL118W RHO3 Ras HOmolog YIL120W QDR1 QuiniDine Resistance YIL121W QDR2 QuiniDine Resistance YIL130W ASG1 Activator of Stress Genes YIL131C FKH1 ForK head Homolog YIL133C RPL16A Ribosomal Protein of the Large subunit YIL146C ATG32 AuTophaGy related YIL148W RPL40A Ribosomal Protein of the Large subunit YIL159W BNR1 BNi1 Related YIL160C POT1 Peroxisomal Oxoacyl Thiolase YIL164C NIT1 NITrilase superfamily YIL165C YIR016W YIR017C MET28 METhionine YIR018W YAP5 Yeast AP-1 YIR027C DAL1 Degradation of Allantoin YIR028W DAL4 Degradation of Allantoin YIR029W DAL2 Degradation of Allantoin YIR030C DCG1 Dal80p-Controlled Gene YIR031C DAL7 Degradation of Allantoin YIR032C DAL3 Degradation of Allantoin YIR033W MGA2 Multicopy suppressor of GAm1 (snf2) YIR034C LYS1 LYSine requiring YJL006C CTK2 Carboxy-Terminal domain Kinase YJL011C RPC17 RNA Polymerase C YJL026W RNR2 RiboNucleotide Reductase YJL028W YJL029C VPS53 Vacuolar Protein Sorting YJL034W KAR2 KARyogamy YJL042W MHP1 MAP-Homologous Protein YJL043W YJL044C GYP6 Gtpase-activating protein of Ypt6 Protein YJL047C-A YJL048C UBX6 UBiquitin regulatory X YJL076W NET1 Nucleolar silencing Establishing factor and Telophase regulator YJL082W IML2 Increased Minichromosome Loss YJL083W TAX4 YJL084C ALY2 Arrestin-Like Yeast protein YJL088W ARG3 ARGinine requiring YJL089W SIP4 SNF1-Interacting Protein YJL101C GSH1 glutathione (GSH) YJL107C YJL110C GZF3 Gata Zinc Finger protein

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YJL115W ASF1 Anti-Silencing Function YJL117W PHO86 PHOsphate metabolism YJL127C-B YJL130C URA2 URAcil requiring YJL133C-A YJL134W LCB3 Long-Chain Base YJL136C RPS21B Ribosomal Protein of the Small subunit YJL141C YAK1 Yet Another Kinase YJL148W RPA34 RNA Polymerase A YJL149W DAS1 Dst1-delta 6-Azauracil Sensitivity YJL151C SNA3 Sensitivity to NA+ YJL153C INO1 INOsitol requiring YJL154C VPS35 Vacuolar Protein Sorting YJL157C FAR1 Factor ARrest YJL158C CIS3 CIk1 Suppressing YJL159W HSP150 Heat Shock Protein YJL163C YJL171C TOH1 TOS One Homolog YJL172W CPS1 CarboxyPeptidase yscS YJL177W RPL17B Ribosomal Protein of the Large subunit YJL178C ATG27 AuTophaGy related YJL186W MNN5 MaNNosyltransferase YJL187C SWE1 Saccharomyces WEe1 YJL189W RPL39 Ribosomal Protein of the Large subunit YJL190C RPS22A Ribosomal Protein of the Small subunit YJL192C SOP4 Suppressor Of Pma1-7 YJL194W CDC6 Cell Division Cycle YJL196C ELO1 ELOngation defective YJL200C ACO2 ACOnitase YJL210W PEX2 PEroXin YJL212C OPT1 OligoPeptide Transporter YJL217W REE1 REgulation of Enolase YJR001W AVT1 Amino acid Vacuolar Transport YJR008W MHO1 Memo HOmolog YJR016C ILV3 IsoLeucine-plus-Valine requiring YJR025C BNA1 Biosynthesis of Nicotinic Acid YJR045C SSC1 Stress-Seventy subfamily C YJR046W TAH11 Topo-A Hypersensitive YJR047C ANB1 ANaeroBically induced YJR048W CYC1 CYtochrome C YJR052W RAD7 RADiation sensitive YJR055W HIT1 HIgh Temperature growth YJR059W PTK2 Putative serine/Threonine protein Kinase YJR072C NPA3 Nucleolar Preribosomal Associated YJR073C OPI3 OverProducer of Inositol YJR074W MOG1 Multicopy suppressor Of ts Gsp1 YJR077C MIR1 Mitochondrial Import Receptor YJR092W BUD4 BUD site selection YJR094W-A RPL43B Ribosomal Protein of the Large subunit

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YJR101W RSM26 Ribosomal Small subunit of Mitochondria YJR103W URA8 URAcil requiring YJR104C SOD1 SuperOxide Dismutase YJR105W ADO1 ADenOsine kinase YJR109C CPA2 Carbamyl Phosphate synthetase A YJR110W YMR1 Yeast Myotubularin Related YJR111C PXP2 PeroXisomal Protein YJR113C RSM7 Ribosomal Small subunit of Mitochondria YJR119C JHD2 JmjC domain-containing Histone Demethylase YJR123W RPS5 Ribosomal Protein of the Small subunit YJR127C RSF2 ReSpiration Factor YJR137C MET5 METhionine requiring YJR139C HOM6 HOMoserine requiring YJR145C RPS4A Ribosomal Protein of the Small subunit YJR147W HMS2 High-copy Mep Suppressor YJR148W BAT2 Branched-chain Amino acid Transaminase YJR149W YJR152W DAL5 Degradation of Allantoin YKL001C MET14 METhionine requiring YKL006W RPL14A Ribosomal Protein of the Large subunit YKL007W CAP1 CAPping YKL008C LAC1 Longevity-Assurance gene Cognate (LAG1 Cognate) YKL015W PUT3 Proline UTilization YKL016C ATP7 ATP synthase YKL023C-A YKL023W YKL029C MAE1 MAlic Enzyme YKL032C IXR1 Intrastrand cross (X)-link Recognition YKL035W UGP1 UDP-glucose pyrophosphorylase YKL051W SFK1 Suppressor of Four Kinase YKL052C ASK1 Associated with Spindles and Kinetochores YKL056C TMA19 Translation Machinery Associated YKL057C NUP120 NUclear Pore YKL060C FBA1 Fructose-1,6-Bisphosphate Aldolase YKL062W MSN4 Multicopy suppressor of SNF1 mutation YKL063C YKL068W-A YKL080W VMA5 Vacuolar Membrane Atpase YKL081W TEF4 Translation Elongation Factor YKL096C-B YKL096W-A CWP2 Cell Wall Protein YKL103C APE1 AminoPeptidase YKL110C KTI12 Kluveromyces lactis Toxin Insensitive YKL120W OAC1 OxaloAcetate Carrier YKL142W MRP8 Mitochondrial Ribosomal Protein YKL152C GPM1 Glycerate PhosphoMutase YKL171W NNK1 Nitrogen Network Kinase YKL180W RPL17A Ribosomal Protein of the Large subunit YKL183W LOT5 LOw Temperature-responsive

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YKL186C MTR2 Mrna TRansport YKL201C MNN4 MaNNosyltransferase YKL210W UBA1 UBiquitin Activating YKL211C TRP3 TRyPtophan YKL216W URA1 URAcil requiring YKR003W OSH6 OxySterol binding protein Homolog YKR004C ECM9 ExtraCellular Mutant YKR009C FOX2 Fatty acid OXidation YKR011C YKR013W PRY2 Pathogen Related in Yeast YKR024C DBP7 Dead Box Protein YKR031C SPO14 SPOrulation YKR034W DAL80 Degradation of Allantoin YKR035W-A DID2 Doa4-Independent Degradation YKR038C KAE1 Kinase-Associated Endopeptidase YKR039W GAP1 General Amino acid Permease YKR041W YKR052C MRS4 Mitochondrial RNA Splicing YKR058W GLG1 -Like Gene YKR074W AIM29 Altered Inheritance rate of Mitochondria YKR080W MTD1 Methylene Tetrahydrafolate Dehydrogenase YKR089C TGL4 TriacylGlycerol Lipase YKR092C SRP40 Serine Rich Protein YKR094C RPL40B Ribosomal Protein of the Large subunit YLL012W YEH1 Yeast steryl Ester Hydrolase YLL018C-A COX19 Cytochrome c OXidase YLL024C SSA2 Stress-Seventy subfamily A YLL026W HSP104 Heat Shock Protein YLL027W ISA1 Iron Sulfur Assembly YLL029W FRA1 Fe Repressor of Activation YLL039C UBI4 Ubiquitin YLL045C RPL8B Ribosomal Protein of the Large subunit YLL051C FRE6 Ferric REductase YLL055W YCT1 Yeast Cysteine Transporter YLR018C POM34 POre Membrane YLR023C IZH3 Implicated in Zinc Homeostasis YLR034C SMF3 YLR042C YLR043C TRX1 ThioRedoXin YLR044C PDC1 Pyruvate DeCarboxylase YLR048W RPS0B Ribosomal Protein of the Small subunit YLR053C YLR055C SPT8 SuPpressor of Ty YLR056W ERG3 ERGosterol biosynthesis YLR057W MNL2 MaNnosidase-Like protein YLR058C SHM2 Serine HydroxyMethyltransferase YLR061W RPL22A Ribosomal Protein of the Large subunit YLR074C BUD20 BUD site selection YLR075W RPL10 Ribosomal Protein of the Large subunit

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YLR077W FMP25 Found in Mitochondrial Proteome YLR084C RAX2 YLR089C ALT1 ALanine Transaminase YLR090W XDJ1 YLR092W SUL2 SULfate YLR094C GIS3 GIg1-2 Suppressor YLR099C ICT1 Increased Copper Tolerance YLR099W-A MIM2 YLR100W ERG27 ERGosterol biosynthesis YLR108C YLR109W AHP1 Alkyl HydroPeroxide reductase YLR110C CCW12 Covalently linked Cell Wall protein YLR113W HOG1 High Osmolarity Glycerol response YLR120C YPS1 YaPSin YLR130C ZRT2 Zinc-Regulated Transporter YLR136C TIS11 similar to the mammalian TPA Induced Sequence gene family YLR142W PUT1 Proline UTilization YLR143W DPH6 DiPHthamide biosynthesis YLR149C YLR150W STM1 Suppressor of ToM1 YLR152C YLR153C ACS2 Acetyl CoA Synthetase YLR154C RNH203 RNase H YLR163C MAS1 Mitochondrial ASsembly YLR164W SHH4 SDH4 Homolog YLR167W RPS31 Ribosomal Protein of the Small subunit YLR168C UPS2 UnProceSsed YLR174W IDP2 Isocitrate Dehydrogenase, NADP-specific YLR178C TFS1 cdc Twenty-Five Suppressor YLR179C YLR180W SAM1 S-AdenosylMethionine requiring YLR183C TOS4 Target Of Sbf YLR185W RPL37A Ribosomal Protein of the Large subunit YLR189C ATG26 AuTophaGy related YLR205C HMX1 HeMe oXygenase YLR212C TUB4 TUBulin YLR220W CCC1 Cross-Complements Ca(2+) phenotype of csg1 YLR224W UCC1 Ubiquitination of Citrate synthase in the glyoxylate Cycle YLR225C YLR226W BUR2 Bypass UAS Requirement YLR249W YEF3 Yeast Elongation Factor YLR250W SSP120 Saccharomyces Secretory Protein YLR256W HAP1 Heme Activator Protein YLR257W YLR259C HSP60 Heat Shock Protein YLR264C-A YLR278C YLR284C ECI1 Enoyl-CoA Isomerase YLR287C-A RPS30A Ribosomal Protein of the Small subunit

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YLR301W HRI1 HRr25 Interacting YLR303W MET17 METhionine requiring YLR304C ACO1 ACOnitase YLR312C ATG39 AuTophaGy related YLR312W-A MRPL15 Mitochondrial Ribosomal Protein, Large subunit YLR325C RPL38 Ribosomal Protein of the Large subunit YLR326W YLR327C TMA10 Translation Machinery Associated YLR333C RPS25B Ribosomal Protein of the Small subunit YLR335W NUP2 NUclear Pore YLR340W RPP0 Ribosomal Protein P0 YLR344W RPL26A Ribosomal Protein of the Large subunit YLR346C CIS1 CItrinin Sensitive knockout YLR347C KAP95 KAryoPherin YLR348C DIC1 DIcarboxylate Carrier YLR350W ORM2 YLR354C TAL1 TransALdolase YLR355C ILV5 IsoLeucine-plus-Valine requiring YLR373C VID22 Vacuolar Import and Degradation YLR380W CSR1 Chs5 Spa2 Rescue YLR387C REH1 REI1 Homolog YLR388W RPS29A Ribosomal Protein of the Small subunit YLR389C STE23 STErile YLR390W-A CCW14 Covalently linked Cell Wall protein YLR399C BDF1 BromoDomain Factor YLR401C DUS3 DihydroUridine Synthase YLR406C RPL31B Ribosomal Protein of the Large subunit YLR406C-A YLR412C-A YLR414C PUN1 Plasma membrane protein Upregulated during Nitrogen stress YLR415C YLR436C ECM30 ExtraCellular Mutant YLR437C DIF1 Damage-regulated Import Facilitator YLR438W CAR2 Catabolism of ARginine YLR439W MRPL4 Mitochondrial Ribosomal Protein, Large subunit YLR441C RPS1A Ribosomal Protein of the Small subunit YLR448W RPL6B Ribosomal Protein of the Large subunit YLR452C SST2 SuperSensiTive YLR454W FMP27 Found in Mitochondrial Proteome YML007C-A YML007W YAP1 Yeast AP-1 YML008C ERG6 ERGosterol biosynthesis YML017W PSP2 Polymerase SuPpressor YML018C YML024W RPS17A Ribosomal Protein of the Small subunit YML025C YML6 YML026C RPS18B Ribosomal Protein of the Small subunit YML028W TSA1 Thiol-Specific Antioxidant YML034W SRC1 Spliced mRNA and Cell cycle regulated gene

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YML052W SUR7 SUppressor of Rvs167 mutation YML053C YML054C CYB2 CYtochrome B YML057W CMP2 CalModulin binding Protein YML058W SML1 Suppressor of Mec1 Lethality YML058W-A HUG1 YML059C NTE1 Neuropathy Target Esterase YML063W RPS1B Ribosomal Protein of the Small subunit YML064C TEM1 TErmination of M phase YML073C RPL6A Ribosomal Protein of the Large subunit YML088W UFO1 UV-F-box-HO YML098W TAF13 TATA binding protein-Associated Factor YML099C ARG81 ARGinine requiring YML100W TSL1 Trehalose Synthase Long chain YML100W-A YML101C CUE4 Coupling of Ubiquitin conjugation to ER degradation YML111W BUL2 Binds Ubiquitin Ligase YML121W GTR1 GTp binding protein Resemblance YMR001C-A YMR002W MIX17 Mitochondrial Intermembrane space CX(n)C motif protein YMR006C PLB2 PhosphoLipase B YMR013C SEC59 SECretory YMR014W BUD22 BUD site selection YMR015C ERG5 ERGosterol biosynthesis YMR031C EIS1 EISosome YMR032W HOF1 Homolog Of cdc Fifteen YMR041C ARA2 ARAbinose YMR042W ARG80 ARGinine requiring YMR043W MCM1 MiniChromosome Maintenance YMR052W FAR3 Factor ARrest YMR056C AAC1 ADP/ATP Carrier YMR058W FET3 FErrous Transport YMR062C ARG7 ARGinine requiring YMR072W ABF2 ARS-Binding Factor YMR083W ADH3 Alcohol DeHydrogenase YMR086W SEG1 Stability of Eisosomes Guaranteed YMR088C VBA1 Vacuolar Basic Amino acid transporter YMR095C SNO1 SNZ proximal Open reading frame YMR096W SNZ1 SNooZe YMR107W SPG4 Stationary Phase Gene YMR108W ILV2 IsoLeucine-plus-Valine requiring YMR116C ASC1 Absence of growth Suppressor of Cyp1 YMR120C ADE17 ADEnine YMR121C RPL15B Ribosomal Protein of the Large subunit YMR122W-A Novel Cell Wall protein YMR135C GID8 Glucose Induced Degradation deficient YMR136W GAT2 YMR142C RPL13B Ribosomal Protein of the Large subunit YMR143W RPS16A Ribosomal Protein of the Small subunit

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YMR144W FDO1 Forkhead one interacting protein involved in DOnor preference YMR173W DDR48 DNA Damage Responsive YMR182W-A YMR183C SSO2 Supressor of Sec One YMR186W HSC82 YMR188C MRPS17 Mitochondrial Ribosomal Protein, Small subunit YMR189W GCV2 GlyCine cleaVage YMR194C-B CMC4 Cx9C Motif-Containing protein YMR195W ICY1 Interacting with the CYtoskeleton YMR201C RAD14 RADiation sensitive YMR202W ERG2 ERGosterol biosynthesis YMR205C PFK2 PhosphoFructoKinase YMR216C SKY1 SRPK1-like Kinase in Yeast YMR217W GUA1 GUanine Auxotroph YMR238W DFG5 Defective for Filamentous Growth YMR240C CUS1 Cold sensitive U2 snRNA Suppressor YMR241W YHM2 Yeast suppressor of HM mutant YMR242C RPL20A Ribosomal Protein of the Large subunit YMR243C ZRC1 Zinc Resistance Conferring YMR244C-A COA6 Cytochrome Oxidase Assembly YMR246W FAA4 Fatty Acid Activation YMR251W-A HOR7 HyperOsmolarity-Responsive YMR253C YMR265C YMR266W RSN1 Rescue of Sro7 at high Nacl YMR272C SCS7 Suppressor of Ca2+ Sensitivity YMR290C HAS1 Helicase Associated with Set1 YMR291W TDA1 Topoisomerase I Damage Affected YMR296C LCB1 Long-Chain Base YMR302C YME2 Yeast Mitochondrial Escape YMR306W FKS3 FK506 Sensitivity YMR307W GAS1 Glycophospholipid-Anchored Surface protein YMR313C TGL3 TriacylGlycerol Lipase YMR314W PRE5 PRoteinase yscE YMR315W YMR318C ADH6 Alcohol DeHydrogenase YNL006W LST8 Lethal with Sec Thirteen YNL007C SIS1 SIt4 Suppressor YNL015W PBI2 Proteinase B Inhibitor YNL016W PUB1 PolyUridylate Binding YNL029C KTR5 Kre Two Related YNL030W HHF2 Histone H Four YNL031C HHT2 Histone H Three YNL036W NCE103 NonClassical Export YNL037C IDH1 Isocitrate DeHydrogenase YNL042W BOP3 Bypass Of Pam1 YNL053W MSG5 Multicopy Suppressor of GPA1 YNL055C POR1 PORin YNL065W AQR1 Acids Quinidine Resistance

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YNL066W SUN4 Sim1 Uth1 Nca3 YNL067W RPL9B Ribosomal Protein of the Large subunit YNL067W-B YNL069C RPL16B Ribosomal Protein of the Large subunit YNL077W APJ1 Anti-Prion DnaJ YNL079C TPM1 TroPoMyosin YNL080C EOS1 ER-localized and Oxidants Sensitive YNL087W TCB2 Three Calcium and lipid Binding domains (TriCalBins) YNL096C RPS7B Ribosomal Protein of the Small subunit YNL097C PHO23 PHOsphate metabolism YNL097C-B YNL098C RAS2 homologous to RAS proto-oncogene YNL101W AVT4 Amino acid Vacuolar Transport YNL103W MET4 METhionine requiring YNL104C LEU4 LEUcine biosynthesis YNL118C DCP2 mRNA DeCaPping YNL124W NAF1 Nuclear Assembly Factor YNL125C ESBP6 YNL129W NRK1 Nicotinamide Riboside Kinase YNL130C CPT1 CholinePhosphoTransferase YNL132W KRE33 Killer toxin REsistant YNL133C FYV6 Function required for Yeast Viability YNL134C YNL135C FPR1 Fk 506-sensitive Proline Rotamase YNL141W AAH1 Adenine AminoHydrolase YNL142W MEP2 YNL147W LSM7 Like SM YNL149C PGA2 Processing of Gas1p and ALP YNL160W YGP1 Yeast GlycoProtein YNL162W RPL42A Ribosomal Protein of the Large subunit YNL169C PSD1 PhosphatidylSerine Decarboxylase YNL172W APC1 Anaphase Promoting Complex subunit YNL173C MDG1 Multicopy suppressor of Defective G-protein YNL176C TDA7 Topoisomerase I Damage Affected YNL178W RPS3 Ribosomal Protein of the Small subunit YNL180C RHO5 Ras HOmolog YNL182C IPI3 Involved in Processing ITS2 YNL183C NPR1 Nitrogen Permease Reactivator YNL186W UBP10 UBiquitin-specific Protease YNL190W YNL191W DUG3 Deficient in Utilization of Glutathione YNL193W YNL208W YNL216W RAP1 Repressor/Activator site binding Protein YNL217W YNL220W ADE12 ADEnine requiring YNL221C POP1 Processing Of Precursor RNAs YNL234W YNL239W LAP3 Leucine AminoPeptidases

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YNL240C NAR1 Nuclear Architecture Related YNL241C ZWF1 ZWischenFerment YNL251C NRD1 Nuclear pre-mRNA Down-regulation YNL268W LYP1 LYsine-specific Permease YNL277W MET2 METhionine requiring YNL278W CAF120 CCR4 Associated Factor YNL279W PRM1 Pheromone-Regulated Membrane protein YNL280C ERG24 ERGosterol biosynthesis YNL281W HCH1 High-Copy Hsp90 suppressor YNL282W POP3 Processing Of Precursor RNAs YNL288W CAF40 CCR4 Associated Factor YNL289W PCL1 Pho85 CycLin YNL298W CLA4 CLn Activity dependant YNL302C RPS19B Ribosomal Protein of the Small subunit YNL311C SKP2 homology with human SKP2 YNL327W EGT2 Early G1 Transcript YNR001C CIT1 CITrate synthase YNR002C ATO2 Ammonia (Ammonium) Transport Outward YNR009W NRM1 Negative Regulator of MBF targets YNR011C PRP2 Pre-mRNA Processing YNR012W URK1 URidine Kinase YNR013C PHO91 PHOsphate metabolism YNR014W YNR017W TIM23 Translocase of the Inner Mitochondrial membrane YNR018W RCF2 Respiratory superComplex Factor YNR019W ARE2 Acyl-coenzyme A: cholesterol acyl transferase-Related Enzyme YNR028W CPR8 Cyclosporin-sensitive Proline Rotamase YNR050C LYS9 LYSine requiring YOL006C TOP1 TOPoisomerase YOL011W PLB3 PhosphoLipase B YOL012C HTZ1 Histone Two A Z1 YOL019W YOL019W-A YOL021C DIS3 homolog of S. pombe dis3 (chromosome DISjunction) YOL025W LAG2 Longevity Assurance Gene YOL026C MIM1 Mitochondrial IMport YOL030W GAS5 Glycophospholipid-Anchored Surface protein YOL031C SIL1 Suppressor of the Ire1/Lhs1 double mutant YOL039W RPP2A Ribosomal Protein P2 Alpha YOL040C RPS15 Ribosomal Protein of the Small subunit YOL052C SPE2 SPErmidine auxotroph YOL052C-A DDR2 DNA Damage Responsive YOL057W YOL058W ARG1 ARGinine requiring YOL059W GPD2 Glycerol-3-Phosphate Dehydrogenase YOL060C MAM3 YOL064C MET22 METhionine requiring YOL086C ADH1 Alcohol DeHydrogenase YOL107W

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YOL109W ZEO1 ZEOcin resistance YOL110W SHR5 Suppressor of Hyperactive Ras YOL111C MDY2 Mating-Deficient Yeast YOL113W SKM1 STE20/PAK homologous Kinase related to Morphogenesis YOL114C PTH4 peptidyl tRNA hydrolase 4 YOL117W RRI2 YOL119C MCH4 MonoCarboxylate transporter Homolog YOL120C RPL18A Ribosomal Protein of the Large subunit YOL121C RPS19A Ribosomal Protein of the Small subunit YOL125W TRM13 TRna Methyltransferase YOL126C MDH2 Malate DeHydrogenase YOL127W RPL25 Ribosomal Protein of the Large subunit YOL128C YGK3 Yeast homolog of Kinase YOL140W ARG8 ARGinine requiring YOL151W GRE2 Genes de Respuesta a Estres (stress responsive genes) YOL158C ENB1 ENteroBactin YOR007C SGT2 Small Glutamine-rich Tetratricopeptide repeat-containing protein YOR023C AHC1 Ada Histone acetyltransferase complex Component YOR027W STI1 STress Inducible YOR032C HMS1 High-copy Mep Suppressor YOR032W-A YOR042W CUE5 Coupling of Ubiquitin conjugation to ER degradation YOR051C ETT1 Enhancer of Translation Termination 1 YOR052C TMC1 Trivalent Metalloid sensitive, Cuz1-related protein YOR062C YOR063W RPL3 Ribosomal Protein of the Large subunit YOR064C YNG1 Yeast iNG1 homolog YOR073W SGO1 ShuGOshin (Japanese for "guardian spirit") YOR078W BUD21 BUD site selection YOR087W YVC1 Yeast Vacuolar Conductance YOR096W RPS7A Ribosomal Protein of the Small subunit YOR099W KTR1 Kre Two Related YOR100C CRC1 CaRnitine Carrier YOR101W RAS1 homologous to RAS proto-oncogene YOR108W LEU9 LEUcine biosynthesis YOR130C ORT1 ORnithine Transporter YOR138C RUP1 Rsp5-Ubp2 interacting Protein YOR182C RPS30B Ribosomal Protein of the Small subunit YOR184W SER1 SERine requiring YOR185C GSP2 Genetic Suppressor of Prp20-1 YOR187W TUF1 YOR193W PEX27 PEroXisome related YOR221C MCT1 Malonyl-CoA:ACP Transferase YOR222W ODC2 OxoDicarboxylate Carrier YOR226C ISU2 IscU homolog YOR227W HER1 Hmg2p ER Remodeling YOR229W WTM2 WD repeat containing Transcriptional Modulator YOR230W WTM1 WD repeat containing Transcriptional Modulator YOR231W MKK1 Mitogen-activated protein Kinase-Kinase

S1 Table S1 Table

Dal80 Prom (1269) Peak Calling YOR234C RPL33B Ribosomal Protein of the Large subunit YOR236W DFR1 DihydroFolate Reductase YOR246C ENV9 late ENdosome and Vacuole interface function YOR268C YOR269W PAC1 Perish in the Absence of Cin8p YOR270C VPH1 Vacuolar pH YOR271C FSF1 Fungal SideroFlexin 1 YOR272W YTM1 YOR273C TPO4 Transporter of POlyamines YOR274W MOD5 tRNA MODification YOR292C YOR293W RPS10A Ribosomal Protein of the Small subunit YOR298C-A MBF1 Multiprotein Bridging Factor YOR299W BUD7 BUD site selection YOR302W YOR303W CPA1 Carbamyl Phosphate synthetase A YOR304W ISW2 Imitation SWitch subfamily YOR306C MCH5 MonoCarboxylate transporter Homolog YOR312C RPL20B Ribosomal Protein of the Large subunit YOR315W SFG1 SuperFicial pseudohyphal Growth YOR316C COT1 CObalt Toxicity YOR316C-A YOR317W FAA1 Fatty Acid Activation YOR319W HSH49 Human Sap Homolog YOR324C FRT1 Functionally Related to TCP1 YOR327C SNC2 Suppressor of the Null allele of CAP YOR335C ALA1 ALAnyl-tRNA synthetase YOR337W TEA1 Ty Enhancer Activator YOR338W YOR340C RPA43 RNA Polymerase A YOR342C YOR344C TYE7 Ty1-mediated Expression YOR347C PYK2 PYruvate Kinase YOR348C PUT4 Proline UTilization YOR349W CIN1 Chromosome INstability YOR356W CIR2 Changed Intracellular Redox state YOR363C PIP2 Peroxisome Induction Pathway YOR369C RPS12 Ribosomal Protein of the Small subunit YOR373W NUD1 YOR374W ALD4 ALdehyde Dehydrogenase YOR375C GDH1 Glutamate DeHydrogenase YOR378W AMF1 AMmonium Facilitator YOR382W FIT2 Facilitator of Iron Transport YPL004C LSP1 Long chain bases Stimulate Phosphorylation YPL014W CIP1 Cdk1 Interacting Protein YPL015C HST2 Homolog of SIR Two (SIR2) YPL016W SWI1 SWItching deficient YPL017C IRC15 Increased Recombination Centers YPL018W CTF19 Chromosome Transmission Fidelity

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Dal80 Prom (1269) Peak Calling YPL019C VTC3 Vacuolar Transporter Chaperone YPL024W RMI1 RecQ Mediated genome Instability YPL026C SKS1 Suppressor Kinase of SNF3 YPL037C EGD1 Enhancer of Gal4 DNA binding YPL048W CAM1 Calcium And Membrane-binding protein YPL049C DIG1 Down-regulator of Invasive Growth YPL055C LGE1 LarGE cells YPL056C LCL1 Long Chronological Lifespan YPL057C SUR1 SUppressor of Rvs161 and rvs167 mutations YPL061W ALD6 ALdehyde Dehydrogenase YPL067C Histidine Triad with Channel YPL068C YPL075W GCR1 GlyColysis Regulation YPL079W RPL21B Ribosomal Protein of the Large subunit YPL081W RPS9A Ribosomal Protein of the Small subunit YPL082C MOT1 Modifier of Transcription YPL088W YPL089C RLM1 Resistance to Lethality of MKK1P386 overexpression YPL090C RPS6A Ribosomal Protein of the Small subunit YPL092W SSU1 Sensitive to SUlfite YPL093W NOG1 NucleOlar G-protein YPL095C EEB1 Ethyl Ester Biosynthesis YPL106C SSE1 Stress Seventy subfamily E YPL111W CAR1 Catabolism of ARginine YPL112C PEX25 PEroXisome related YPL117C IDI1 Isopentenyl Diphosphate Isomerase YPL126W NAN1 Net1 Associated Nuclear protein YPL127C HHO1 Histone H One YPL128C TBF1 TTAGGG repeat-Binding Factor YPL131W RPL5 Ribosomal Protein of the Large subunit YPL135W ISU1 IScU homolog YPL137C GIP3 Glc7 Interacting Protein YPL143W RPL33A Ribosomal Protein of the Large subunit YPL144W POC4 PrOteasome Chaperone YPL155C KIP2 KInesin related Protein YPL163C SVS1 Suppressor of Vanadate Sensitivity YPL170W DAP1 DAmage resistance Protein YPL177C CUP9 YPL187W MF(ALPHA)1 Mating Factor ALPHA YPL189C-A COA2 Cytochrome Oxidase Assembly YPL189W GUP2 Glycerol UPtake YPL198W RPL7B Ribosomal Protein of the Large subunit YPL199C YPL202C AFT2 Activator of Fe (iron) Transcription YPL207W TYW1 Trna-YW synthesizing protein YPL221W FLC1 FLavin Carrier YPL222W FMP40 Found in Mitochondrial Proteome YPL229W YPL231W FAS2 Fatty Acid Synthetase

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Dal80 Prom (1269) Peak Calling YPL232W SSO1 Supressor of Sec One YPL240C HSP82 Heat Shock Protein YPL249C-A RPL36B Ribosomal Protein of the Large subunit YPL250C ATG41 AuTophaGy related YPL252C YAH1 Yeast Adrenodoxin Homolog YPL264C YPL265W DIP5 DIcarboxylic amino acid Permease YPL273W SAM4 S-AdenosylMethionine metabolism YPL274W SAM3 S-AdenosylMethionine metabolism YPR005C HAL1 HALotolerance YPR009W SUT2 Sterol UpTake YPR010C RPA135 RNA Polymerase A YPR010C-A YPR028W YOP1 YIP One Partner YPR030W CSR2 Chs5 Spa2 Rescue YPR035W GLN1 GLutamiNe metabolism YPR036W VMA13 Vacuolar Membrane Atpase YPR036W-A SPO24 SPOrulation YPR042C PUF2 PUmilio-homology domain Family YPR043W RPL43A Ribosomal Protein of the Large subunit YPR054W SMK1 YPR058W YMC1 Yeast Mitochondrial Carrier YPR063C YPR065W ROX1 Regulation by OXygen YPR074C TKL1 TransKetoLase YPR080W TEF1 Translation Elongation Factor YPR102C RPL11A Ribosomal Protein of the Large subunit YPR103W PRE2 PRoteinase yscE YPR127W YPR131C NAT3 N-terminal AcetylTransferase YPR132W RPS23B Ribosomal Protein of the Small subunit YPR138C MEP3 YPR144C NOC4 NucleOlar Complex associated YPR145W ASN1 ASparagiNe requiring YPR149W NCE102 NonClassical Export YPR151C SUE1 YPR158W CUR1 Curing of [URe3] YPR159C-A YPR161C SGV1 Suppressor of Gpa1-Val50 mutation YPR166C MRP2 Mitochondrial Ribosomal Protein YPR167C MET16 METhionine requiring YPR168W NUT2 Negative regulation of URS Two YPR184W GDB1 Glycogen DeBranching YPR192W AQY1 AQuaporin from Yeast

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