Input Cluster (n=199) YAL003W EFB1 YAL005C SSA1 YAL025C MAK16 YAL039C CYC3 YBL029W YBL038W MRPL16 YBL039C URA7 YBL074C AAR2 YBL098W BNA4 YBR031W RPL4A YBR040W FIG1 YBR082C UBC4 YBR086C IST2 YBR087W RFC5 YBR105C VID24 YBR239C YCL038C AUT4 YCL048W YCL073C YCR015C YCR024C YCR024C-A PMP1 YCR066W RAD18 YCR090C YDL047W SIT4 YDL055C PSA1 YDL139C SCM3 YDL140C RPO21 YDL185W TFP1 YDR001C NTH1 YDR002W YRB1 YDR023W SES1 YDR052C DBF4 YDR096W GIS1 YDR184C ATC1 YDR214W AHA1 YDR277C MTH1 YDR311W TFB1 YDR322W MRPL35 YDR342C HXT7 YDR343C HXT6 YDR399W HPT1 YDR523C SPS1 YDR524C AGE1 YEL027W CUP5 YEL032W MCM3 YER036C KRE30 YER037W PHM8 YER089C PTC2 YER090W TRP2 YER110C KAP123 YER132C PMD1 YER159C BUR6 YER165W PAB1 YER169W RPH1 YFL022C FRS2 YFR001W LOC1 YFR055W YGL001C ERG26 YGL008C PMA1 YGL014W PUF4 YGL015C YGL215W CLG1 YGL223C COG1 YGR033C YGR034W RPL26B YGR068C YGR078C PAC10 YGR125W YGR162W TIF4631 YGR170W PSD2 YGR177C ATF2 YGR187C HGH1 YGR195W SKI6 YGR206W YGR229C SMI1 YGR240C PFK1 YGR258C RAD2 YHL011C PRS3 YHR007C ERG11 YHR009C YHR022C YHR032W YHR052W CIC1 YHR071W PCL5 YHR082C KSP1 YHR149C YHR150W YHR205W SCH9 YIL061C SNP1 YIL066C RNR3 YIL108W YIL130W GIN1 YIL131C FKH1 YJL037W YJL038C YJL044C GYP6 YJL165C HAL5 YJL193W YJR001W YJR047C ANB1 YJR048W CYC1 YJR103W URA8 YKL007W CAP1 YKL008C LAC1 YKL027W YKL042W SPC42 YKL056C YKL068W NUP100 YKL079W SMY1 YKL096W CWP1 YKL108W SLD2 YKL109W HAP4 YKL217W JEN1 YKR041W YKR075C YKR098C UBP11 YKR099W BAS1 YKR106W YLL031C GPI13 YLL045C RPL8B YLR018C POM34 YLR022C YLR074C BUD20 YLR075W RPL10 YLR179C YLR180W SAM1 YLR224W YLR249W YEF3 YLR277C YSH1 YLR278C YLR328W NMA1 YLR431C YLR432W IMD3 YLR446W YML043C RRN11 YML055W SPC2 YML056C IMD4 YML121W GTR1 YMR037C MSN2 YMR043W MCM1 YMR070W MOT3 YMR081C ISF1 YMR108W ILV2 YMR146C TIF34 YMR147W YMR171C YMR172W HOT1 YMR180C CTL1 YMR182C RGM1 YMR205C PFK2 YMR216C SKY1 YMR244W YMR296C LCB1 YNL112W DBP2 YNL141W AAH1 YNL180C RHO5 YNL190W YNL209W SSB2 YNL308C KRI1 YNR003C RPC34 YNR004W YNR013C PHO91 YNR017W MAS6 YNR048W YOL006C TOP1 YOL052C SPE2 YOL059W GPD2 YOL105C WSC3 YOR051C YOR054C YOR178C GAC1 YOR270C VPH1 YOR291W YOR307C SLY41 YOR341W RPA190 YOR342C YOR355W GDS1 YOR370C MRS6 YOR389W YPL081W RPS9A YPL116W HOS3 YPL183C YPL184C YPL189W GUP2 YPL277C YPR001W CIT3 YPR008W HAA1 YPR022C YPR028W YOP1 YPR035W GLN1 YPR036W VMA13 YPR060C ARO7 YPR078C YPR079W MRL1 YPR080W TEF1 YPR119W CLB2 YPR144C UTP19 YPR149W NCE102 Genes Not Found: YHR214C-B MIPS Functional Classification Category p-value In Category from Cluster k f cytoplasm 0.000266745 EFB1 SSA1 URA7 RPL4A UBC4 NTH1 YRB1 SES1 MCM3 TRP2 KAP123 PAB1 FRS2 RPL26B PAC10 TIF4631 PFK1 RNR3 ANB1 YKL056C RPL8B RPL10 YEF3 MSN2 TIF34 PFK2 SSB2 GAC1 MRS6 RPS9A GLN1 ARO7 TEF1 33 554 homeostasis of protons 0.000714585 PMP1 TFP1 CUP5 PMA1 VPH1 VMA13 6 35 other cation transporters (Na, K, Ca , NH4, etc.) 0.00112286 PMP1 TFP1 CUP5 PMA1 VPH1 VMA13 6 38 transport ATPases 0.00245165 PMP1 TFP1 CUP5 PMA1 VPH1 VMA13 6 44 translation 0.00392687 EFB1 PAB1 TIF4631 ANB1 YEF3 TIF34 TEF1 7 64 TRANSPORT FACILITATION 0.00458684 AUT4 YCL073C PMP1 TFP1 HXT7 HXT6 CUP5 KRE30 PMA1 YHR032W YJR001W JEN1 YKR106W PHO91 MAS6 VPH1 YOR291W GUP2 VMA13 19 312 MIPS Phenotypes Category p-value In Category from Cluster k f other cell wall mutants 0.00205474 URA7 PSA1 SKI6 SMI1 RPL10 YEF3 RPC34 SPE2 8 73 MIPS Subcellular Localization Category p-value In Category from Cluster k f cytoplasm 0.000904915 EFB1 SSA1 URA7 RPL4A UBC4 NTH1 YRB1 SES1 MCM3 TRP2 KAP123 PAB1 FRS2 RPL26B PAC10 TIF4631 PFK1 RNR3 ANB1 YKL056C RPL8B RPL10 YEF3 MSN2 TIF34 PFK2 SSB2 GAC1 MRS6 RPS9A GLN1 ARO7 TEF1 33 593 MIPS Protein Complexes Category p-value In Category from Cluster k f H+-transporting ATPase, vacuolar 0.000768742 TFP1 CUP5 VPH1 VMA13 4 14 Phosphofructokinase 0.00100339 PFK1 PFK2 2 2 Cytoplasmic translation elongation 0.00229957 EFB1 YEF3 TEF1 3 9 eIF4E/eIF4G/Pab1p complex 0.00294706 PAB1 TIF4631 2 3 MIPS Protein Classes Category p-value In Category from Cluster k f Cys2His2 zinc-finger 0.00168984 GIS1 RPH1 MSN2 MOT3 RGM1 YPR022C 6 41 ion-transport ATPases 0.00344674 PMP1 TFP1 CUP5 PMA1 VPH1 VMA13 6 47 GO Molecular Function Category p-value In Category from Cluster k f CTP synthase [GO:0003883] 0.00100339 URA7 URA8 2 2 6-phosphofructokinase [GO:0003872] 0.00100339 PFK1 PFK2 2 2 hydrogen-/sodium-translocating ATPase [GO:0015442] 0.00228972 TFP1 CUP5 PMA1 VPH1 VMA13 5 30 hydrogen-transporting two-sector ATPase [GO:0003936] 0.00228972 TFP1 CUP5 PMA1 VPH1 VMA13 5 30 enzyme [GO:0003824] 0.00238509 SSA1 CYC3 MRPL16 URA7 BNA4 UBC4 RFC5 YCR024C RAD18 SIT4 PSA1 RPO21 TFP1 NTH1 SES1 DBF4 HPT1 SPS1 CUP5 MCM3 KRE30 PTC2 TRP2 FRS2 YFR055W ERG26 PMA1 CLG1 PSD2 ATF2 SKI6 PFK1 RAD2 PRS3 ERG11 PCL5 KSP1 SCH9 RNR3 HAL5 URA8 UBP11 GPI13 SAM1 NMA1 IMD3 IMD4 GTR1 ILV2 CTL1 PFK2 SKY1 LCB1 DBP2 AAH1 RHO5 RPC34 TOP1 SPE2 GPD2 GAC1 VPH1 RPA190 HOS3 CIT3 GLN1 VMA13 ARO7 CLB2 69 1604 translation factor, nucleic acid binding [GO:0008135] 0.00344674 EFB1 TIF4631 ANB1 YEF3 TIF34 TEF1 6 47 GO Biological Process Category p-value In Category from Cluster k f aromatic compound metabolism [GO:0006725] 0.000713767 URA7 TRP2 PRS3 URA8 BAS1 AAH1 ARO7 7 48 cell growth and/or maintenance [GO:0008151] 0.000761256 EFB1 SSA1 MAK16 CYC3 MRPL16 URA7 AAR2 BNA4 RPL4A FIG1 UBC4 IST2 RFC5 VID24 AUT4 YCL073C YCR024C PMP1 RAD18 SIT4 PSA1 RPO21 TFP1 NTH1 YRB1 SES1 DBF4 MTH1 TFB1 MRPL35 HXT7 HXT6 HPT1 SPS1 AGE1 CUP5 MCM3 PTC2 TRP2 KAP123 PMD1 BUR6 PAB1 RPH1 FRS2 LOC1 YFR055W ERG26 PMA1 PUF4 CLG1 COG1 RPL26B PAC10 TIF4631 PSD2 ATF2 SKI6 SMI1 PFK1 RAD2 PRS3 ERG11 CIC1 PCL5 KSP1 SCH9 SNP1 RNR3 FKH1 GYP6 HAL5 ANB1 CYC1 URA8 CAP1 SPC42 NUP100 SMY1 CWP1 SLD2 HAP4 JEN1 BAS1 YKR106W GPI13 RPL8B POM34 BUD20 RPL10 SAM1 YEF3 YSH1 NMA1 IMD3 RRN11 SPC2 GTR1 MSN2 MCM1 MOT3 ISF1 ILV2 TIF34 HOT1 CTL1 RGM1 PFK2 SKY1 LCB1 AAH1 SSB2 KRI1 RPC34 PHO91 MAS6 TOP1 SPE2 GPD2 WSC3 GAC1 VPH1 SLY41 RPA190 GDS1 MRS6 RPS9A CIT3 HAA1 YOP1 GLN1 VMA13 ARO7 YPR078C MRL1 TEF1 CLB2 NCE102 138 3657 regulation of pH [GO:0006885] 0.000971042 TFP1 CUP5 PMA1 VPH1 VMA13 5 25 hydrogen ion homeostasis [GO:0030641] 0.000971042 TFP1 CUP5 PMA1 VPH1 VMA13 5 25 nucleobase metabolism [GO:0009112] 0.00166253 URA7 PRS3 URA8 BAS1 AAH1 5 28 vacuolar acidification [GO:0007035] 0.00262786 TFP1 CUP5 VPH1 VMA13 4 19 nucleobase biosynthesis [GO:0046112] 0.00262786 URA7 PRS3 URA8 BAS1 4 19 monovalent inorganic cation homeostasis [GO:0030004] 0.00266076 TFP1 CUP5 PMA1 VPH1 VMA13 5 31 vacuolar transport [GO:0007034] 0.00307352 TFP1 CUP5 VPH1 VMA13 MRL1 5 32 negative regulation of transcription from Pol II promoter [GO:0000122] 0.00307352 TFB1 BUR6 RPH1 RGM1 GAC1 5 32 biosynthesis [GO:0009058] 0.00446223 EFB1 MRPL16 URA7 BNA4 RPL4A YCR024C PSA1 SES1 MRPL35 HPT1 TRP2 PAB1 FRS2 ERG26 RPL26B TIF4631 PSD2 SMI1 PRS3 ERG11 ANB1 URA8 BAS1 GPI13 RPL8B RPL10 YEF3 IMD3 ILV2 TIF34 LCB1 SSB2 SPE2 RPS9A ARO7 TEF1 36 731 ion homeostasis [GO:0006873] 0.00460405 TFP1 CUP5 YFR055W PMA1 HAL5 SKY1 VPH1 VMA13 8 83 GO Cellular Component Category p-value In Category from Cluster k f 6-phosphofructokinase complex [GO:0005945] 0.00100339 PFK1 PFK2 2 2 hydrogen-translocating V-type ATPase complex [GO:0016471] 0.00132964 TFP1 CUP5 VPH1 VMA13 4 16 cell [GO:0005623] 0.00205075 EFB1 SSA1 MAK16 CYC3 MRPL16 URA7 RPL4A UBC4 RFC5 VID24 YCL073C YCR024C PMP1 RAD18 SIT4 PSA1 RPO21 TFP1 YRB1 SES1 DBF4 TFB1 MRPL35 HXT7 HXT6 CUP5 MCM3 KAP123 BUR6 PAB1 RPH1 FRS2 LOC1 ERG26 PMA1 CLG1 COG1 RPL26B PAC10 TIF4631 PSD2 ATF2 SKI6 SMI1 PFK1 RAD2 PRS3 ERG11 YHR009C CIC1 PCL5 KSP1 SNP1 FKH1 ANB1 CYC1 URA8 CAP1 LAC1 SPC42 NUP100 SMY1 SLD2 HAP4 JEN1 YKR075C BAS1 YKR106W GPI13 RPL8B POM34 BUD20 RPL10 YLR179C SAM1 YEF3 YSH1 IMD3 RRN11 SPC2 GTR1 MSN2 MCM1 MOT3 ILV2 TIF34 HOT1 CTL1 RGM1 PFK2 SKY1 LCB1 DBP2 AAH1 SSB2 KRI1 RPC34 PHO91 MAS6 TOP1 GPD2 WSC3 YOR051C VPH1 RPA190 MRS6 RPS9A HOS3 GUP2 CIT3 HAA1 YOP1 GLN1 VMA13 MRL1 TEF1 CLB2 UTP19 NCE102 119 3106 SMART Domains Category p-value In Category from Cluster k f ZnF_C2H2 0.000917744 GIS1 RPH1 BUD20 MSN2 MOT3 RGM1 YPR022C 7 50 RPOLA_N 0.00294706 RPO21 RPA190 2 3 JmjN 0.00294706 GIS1 RPH1 2 3 PFam-A Domains Category p-value In Category from Cluster k f PF00365 (PFK) 0.00100339 PFK1 PFK2 2 2 PF00096 (zf-C2H2) 0.00192027 GIS1 RPH1 MSN2 MOT3 RGM1 YPR022C 6 42 PF01161 (PBP) 0.00294706 MRPL35 YLR179C 2 3 PF01854 (RNA_pol_A2) 0.00294706 RPO21 RPA190 2 3 PF02375 (jmjN) 0.00294706 GIS1 RPH1 2 3 PF00623 (RNA_pol_A) 0.00294706 RPO21 RPA190 2 3 Yeast Two Hybrid - Uetz Category p-value In Category from Cluster k f Yeast Two Hybrid - Ito (core) Category p-value In Category from Cluster k f YJR103W (URA8) 0.00100339 URA7 URA8 2 2 Yeast Two Hybrid - Ito (full) Category p-value In Category from Cluster k f YJR103W (URA8) 0.00294706 URA7 URA8 2 3 YDR034C (LYS14) 0.00359177 SES1 MTH1 HXT7 YFR055W COG1 NUP100 NMA1 7 63 Synthetic Genetic Array Analysis Category p-value In Category from Cluster k f MDS Proteomics Complexes Category p-value In Category from Cluster k f YOL100W (PKH2) 0.000300886 HXT7 HXT6 YGR033C 3 5 YNL175C (NOP13) 0.000768742 TIF4631 CIC1 IMD3 KRI1 4 14 YLR019W (PSR2) 0.00100339 HXT7 HXT6 2 2 YBL036C 0.00100443 SES1 HXT7 HXT6 3 7 YPL259C (APM1) 0.00262786 PAB1 CIC1 NMA1 KRI1 4 19 Cellzome Complexes Category p-value In Category from Cluster k f YMR205C (PFK2) 0.00100339 PFK1 PFK2 2 2 YGR020C (VMA7) 0.0015696 TFP1 VPH1 VMA13 3 8 YER090W (TRP2) 0.00294706 TRP2 SAM1 2 3 Proteome Localization--Observed Category p-value In Category from Cluster k f cyto 0.00412148 RPL4A PMP1 YCR090C SIT4 PSA1 TFP1 NTH1 YRB1 SES1 HPT1 AGE1 MCM3 PHM8 PTC2 PAB1 FRS2 COG1 RPL26B YGR068C TIF4631 PSD2 ATF2 HGH1 SMI1 PFK1 YHR009C SCH9 RNR3 YIL108W YJR001W YKL056C YKR075C YLR022C RPL10 YLR179C SAM1 YLR224W YEF3 NMA1 YLR431C IMD3 GTR1 ISF1 YMR147W CTL1 PFK2 AAH1 SSB2 YNR004W YOR054C GAC1 MRS6 RPS9A YPL183C YPL184C GLN1 VMA13 TEF1 58 1324 Proteome Localization--Predicted+Observed Category p-value In Category from Cluster k f Deletions Consortium (Essentiality, Morphology) Category p-value In Category from Cluster k f Yeast Fitness Data Category p-value In Category from Cluster k f Published Complexes Category p-value In Category from Cluster k f Harnicharnpai et al. (2001) - Mol Cell 8:505- 0.00403446 SSA1 MAK16 LOC1 CIC1 RPL10 5 34