Input Cluster (n=200) YAL025C MAK16 YAL028W YAL039C CYC3 YAL053W YBL052C SAS3 YBL074C AAR2 YBL098W BNA4 YBR040W FIG1 YBR077C YBR082C UBC4 YBR087W RFC5 YBR105C VID24 YBR239C YBR286W APE3 YBR291C CTP1 YCL048W YCR015C YCR090C YDL035C GPR1 YDL047W SIT4 YDL053C YDL055C PSA1 YDL139C SCM3 YDL140C RPO21 YDL171C GLT1 YDL185W TFP1 YDR001C NTH1 YDR002W YRB1 YDR052C DBF4 YDR096W GIS1 YDR184C ATC1 YDR214W AHA1 YDR216W ADR1 YDR247W YDR277C MTH1 YDR320C SWA2 YDR322W MRPL35 YDR342C HXT7 YDR514C YDR515W SLF1 YDR523C SPS1 YDR524C AGE1 YEL009C GCN4 YEL027W CUP5 YEL032W MCM3 YEL061C CIN8 YER001W MNN1 YER021W RPN3 YER036C KRE30 YER037W PHM8 YER073W ALD5 YER110C KAP123 YER132C PMD1 YER159C BUR6 YER165W PAB1 YER168C CCA1 YFR001W LOC1 YFR055W YGL001C ERG26 YGL006W PMC1 YGL008C PMA1 YGL014W PUF4 YGL015C YGL036W YGL037C PNC1 YGL081W YGL158W RCK1 YGL215W CLG1 YGL216W KIP3 YGL219C MDM34 YGL236C MTO1 YGR033C YGR068C YGR106C YGR109C CLB6 YGR125W YGR127W YGR138C TPO2 YGR170W PSD2 YGR177C ATF2 YGR225W AMA1 YGR240C PFK1 YGR253C PUP2 YHL011C PRS3 YHL024W RIM4 YHR005C GPA1 YHR022C YHR032W YHR052W CIC1 YHR066W SSF1 YHR071W PCL5 YHR082C KSP1 YHR177W YHR205W SCH9 YIL023C YIL060W YIL061C SNP1 YIL084C SDS3 YIL131C FKH1 YIL146C ECM37 YIR006C PAN1 YIR007W YJL016W YJL024C APS3 YJL037W YJL038C YJL190C RPS22A YJL193W YJR047C ANB1 YJR048W CYC1 YJR102C VPS25 YJR103W URA8 YKL027W YKL042W SPC42 YKL079W SMY1 YKL096W CWP1 YKL108W SLD2 YKL139W CTK1 YKR093W PTR2 YKR099W BAS1 YKR106W YLL040C VPS13 YLL045C RPL8B YLR018C POM34 YLR019W PSR2 YLR179C YLR180W SAM1 YLR238W YLR249W YEF3 YLR272C YCS4 YLR277C YSH1 YLR342W FKS1 YLR432W IMD3 YLR455W YML035C AMD1 YML043C RRN11 YML056C IMD4 YML059C YML121W GTR1 YMR004W MVP1 YMR037C MSN2 YMR043W MCM1 YMR081C ISF1 YMR133W REC114 YMR146C TIF34 YMR147W YMR180C CTL1 YMR182C RGM1 YMR205C PFK2 YMR216C SKY1 YMR217W GUA1 YMR244W YMR292W GOT1 YMR319C FET4 YMR321C YNL112W DBP2 YNL141W AAH1 YNL180C RHO5 YNL201C PSY2 YNR003C RPC34 YNR004W YNR013C PHO91 YNR017W MAS6 YNR051C BRE5 YOL006C TOP1 YOL028C YAP7 YOL038W PRE6 YOR044W YOR051C YOR180C DCI1 YOR214C YOR229W WTM2 YOR270C VPH1 YOR307C SLY41 YOR341W RPA190 YOR344C TYE7 YOR349W CIN1 YOR355W GDS1 YOR389W YPL026C SKS1 YPL032C SVL3 YPL081W RPS9A YPL089C RLM1 YPL131W RPL5 YPL160W CDC60 YPL184C YPL189W GUP2 YPL202C AFT2 YPR001W CIT3 YPR008W HAA1 YPR022C YPR028W YOP1 YPR035W GLN1 YPR036W VMA13 YPR060C ARO7 YPR078C YPR079W MRL1 YPR102C RPL11A YPR103W PRE2 YPR149W NCE102 Genes Not Found: MIPS Functional Classification Category p-value In Category from Cluster k f nucleus 0.000309758 MAK16 AAR2 RFC5 YBR239C RPO21 DBF4 ADR1 GCN4 MCM3 CIN8 RPN3 KAP123 BUR6 PAB1 CCA1 KIP3 PUP2 SSF1 KSP1 SNP1 SDS3 FKH1 SLD2 CTK1 BAS1 YCS4 YSH1 RRN11 MSN2 MCM1 REC114 RGM1 DBP2 RPC34 TOP1 YAP7 PRE6 WTM2 RPA190 TYE7 RLM1 PRE2 42 774 vacuolar transport 0.000313629 UBC4 VID24 TFP1 CUP5 PMC1 MVP1 VPH1 VMA13 8 55 ion transporters 0.000776646 CTP1 TFP1 CUP5 PMC1 PMA1 FET4 PHO91 VPH1 VMA13 9 78 other cation transporters (Na, K, Ca , NH4, etc.) 0.00115248 TFP1 CUP5 PMC1 PMA1 VPH1 VMA13 6 38 transport ATPases 0.00251429 TFP1 CUP5 PMC1 PMA1 VPH1 VMA13 6 44 purine ribonucleotide metabolism 0.0028255 PRS3 IMD3 AMD1 IMD4 GUA1 AAH1 6 45 cation transporters 0.00307229 TFP1 CUP5 PMC1 PMA1 FET4 VPH1 VMA13 7 61 sporulation and germination 0.00331737 UBC4 YCL048W SPS1 PMD1 AMA1 PUP2 RIM4 SDS3 MCM1 PRE2 10 114 homeostasis of protons 0.0046866 TFP1 CUP5 PMA1 VPH1 VMA13 5 35 SUBCELLULAR LOCALISATION 0.00480497 MAK16 CYC3 AAR2 FIG1 UBC4 RFC5 VID24 YBR239C APE3 CTP1 GPR1 RPO21 TFP1 NTH1 YRB1 DBF4 ADR1 MRPL35 HXT7 GCN4 CUP5 MCM3 CIN8 MNN1 RPN3 ALD5 KAP123 BUR6 PAB1 CCA1 PMC1 PMA1 KIP3 MTO1 PSD2 PFK1 PUP2 GPA1 SSF1 KSP1 SNP1 SDS3 FKH1 PAN1 RPS22A ANB1 CYC1 SPC42 SMY1 CWP1 SLD2 CTK1 PTR2 BAS1 RPL8B YEF3 YCS4 YSH1 FKS1 RRN11 MVP1 MSN2 MCM1 REC114 TIF34 RGM1 PFK2 FET4 DBP2 RPC34 MAS6 TOP1 YAP7 PRE6 DCI1 WTM2 VPH1 RPA190 TYE7 CIN1 RPS9A RLM1 RPL5 CDC60 CIT3 GLN1 VMA13 ARO7 RPL11A PRE2 90 2256 MIPS Phenotypes Category p-value In Category from Cluster k f MIPS Subcellular Localization Category p-value In Category from Cluster k f nucleus 0.000425759 MAK16 AAR2 RFC5 YBR239C RPO21 DBF4 ATC1 ADR1 GCN4 MCM3 CIN8 RPN3 KAP123 BUR6 PAB1 CCA1 KIP3 PUP2 SSF1 KSP1 SNP1 SDS3 FKH1 CTK1 BAS1 POM34 YCS4 YSH1 RRN11 MSN2 MCM1 REC114 CTL1 RGM1 DBP2 RPC34 TOP1 YAP7 PRE6 WTM2 RPA190 TYE7 RLM1 PRE2 44 836 vacuolar membrane 0.0013264 TFP1 CUP5 PMC1 TPO2 VPH1 VMA13 6 39 vacuole 0.001505 APE3 TFP1 CUP5 PMC1 TPO2 VPH1 VMA13 7 54 MIPS Protein Complexes Category p-value In Category from Cluster k f H+-transporting ATPase, vacuolar 0.000783414 TFP1 CUP5 VPH1 VMA13 4 14 Phosphofructokinase 0.00101352 PFK1 PFK2 2 2 MIPS Protein Classes Category p-value In Category from Cluster k f RAN family 3.20315e-05 YDR247W KSP1 SKS1 3 3 Transcription factors 0.000657145 SAS3 YBR239C GIS1 ADR1 GCN4 FKH1 BAS1 MSN2 MCM1 RGM1 YAP7 TYE7 RLM1 HAA1 YPR022C 15 182 Kinesines 0.00233288 CIN8 KIP3 SMY1 3 9 ion-transport ATPases 0.00353338 TFP1 CUP5 PMC1 PMA1 VPH1 VMA13 6 47 GO Molecular Function Category p-value In Category from Cluster k f protein serine/threonine kinase [GO:0004674] 0.000374008 DBF4 SPS1 RCK1 CLG1 CLB6 PCL5 KSP1 SCH9 CTK1 SKS1 10 86 6-phosphofructokinase [GO:0003872] 0.00101352 PFK1 PFK2 2 2 transferase, transferring phosphorus-containing groups [GO:0016772] 0.0011575 PSA1 RPO21 DBF4 SPS1 CCA1 RCK1 CLG1 CLB6 PFK1 PRS3 PCL5 KSP1 SCH9 CTK1 PFK2 SKY1 RPC34 RPA190 SKS1 19 275 hydrogen-/sodium-translocating ATPase [GO:0015442] 0.00234057 TFP1 CUP5 PMA1 VPH1 VMA13 5 30 hydrogen-transporting two-sector ATPase [GO:0003936] 0.00234057 TFP1 CUP5 PMA1 VPH1 VMA13 5 30 protein kinase [GO:0004672] 0.00296353 DBF4 SPS1 RCK1 CLG1 CLB6 PCL5 KSP1 SCH9 CTK1 SKY1 SKS1 11 131 kinase [GO:0016301] 0.00399507 DBF4 SPS1 RCK1 CLG1 CLB6 PFK1 PRS3 PCL5 KSP1 SCH9 CTK1 PFK2 SKY1 SKS1 14 197 phosphotransferase, alcohol group as acceptor [GO:0016773] 0.00434988 DBF4 SPS1 RCK1 CLG1 CLB6 PFK1 PCL5 KSP1 SCH9 CTK1 PFK2 SKY1 SKS1 13 178 GO Biological Process Category p-value In Category from Cluster k f cell growth and/or maintenance [GO:0008151] 6.3016e-05 MAK16 CYC3 SAS3 AAR2 BNA4 FIG1 UBC4 RFC5 VID24 APE3 CTP1 GPR1 SIT4 PSA1 RPO21 GLT1 TFP1 NTH1 YRB1 DBF4 ADR1 MTH1 SWA2 MRPL35 HXT7 SLF1 SPS1 AGE1 GCN4 CUP5 MCM3 CIN8 MNN1 RPN3 ALD5 KAP123 PMD1 BUR6 PAB1 CCA1 LOC1 YFR055W ERG26 PMC1 PMA1 PUF4 PNC1 RCK1 CLG1 KIP3 MDM34 MTO1 CLB6 PSD2 ATF2 AMA1 PFK1 PUP2 PRS3 RIM4 GPA1 CIC1 SSF1 PCL5 KSP1 SCH9 SNP1 SDS3 FKH1 ECM37 PAN1 APS3 RPS22A ANB1 CYC1 VPS25 URA8 SPC42 SMY1 CWP1 SLD2 CTK1 PTR2 BAS1 YKR106W VPS13 RPL8B POM34 PSR2 SAM1 YEF3 YCS4 YSH1 FKS1 IMD3 AMD1 RRN11 GTR1 MVP1 MSN2 MCM1 ISF1 REC114 TIF34 CTL1 RGM1 PFK2 SKY1 GUA1 GOT1 FET4 AAH1 RPC34 PHO91 MAS6 TOP1 YAP7 PRE6 DCI1 WTM2 VPH1 SLY41 RPA190 TYE7 CIN1 GDS1 SKS1 SVL3 RPS9A RPL5 CDC60 AFT2 CIT3 HAA1 YOP1 GLN1 VMA13 ARO7 YPR078C MRL1 RPL11A PRE2 NCE102 143 3657 ion homeostasis [GO:0006873] 0.000279185 TFP1 SLF1 CUP5 YFR055W PMC1 PMA1 SKY1 VPH1 AFT2 VMA13 10 83 vacuolar transport [GO:0007034] 0.000443623 APE3 TFP1 CUP5 VPH1 VMA13 MRL1 6 32 cation homeostasis [GO:0030003] 0.000474384 TFP1 SLF1 CUP5 YFR055W PMC1 PMA1 VPH1 AFT2 VMA13 9 73 copper homeostasis [GO:0006878] 0.000596423 SLF1 CUP5 YFR055W 3 6 homeostasis [GO:0019725] 0.000765298 TFP1 SLF1 CUP5 YFR055W PMC1 PMA1 SKY1 VPH1 AFT2 VMA13 10 94 hydrogen ion homeostasis [GO:0030641] 0.000993261 TFP1 CUP5 PMA1 VPH1 VMA13 5 25 regulation of pH [GO:0006885] 0.000993261 TFP1 CUP5 PMA1 VPH1 VMA13 5 25 vacuolar acidification [GO:0007035] 0.00267631 TFP1 CUP5 VPH1 VMA13 4 19 monovalent inorganic cation homeostasis [GO:0030004] 0.00271949 TFP1 CUP5 PMA1 VPH1 VMA13 5 31 GO Cellular Component Category p-value In Category from Cluster k f 6-phosphofructokinase complex [GO:0005945] 0.00101352 PFK1 PFK2 2 2 cell [GO:0005623] 0.00103017 MAK16 CYC3 SAS3 YBR077C UBC4 RFC5 VID24 APE3 CTP1 GPR1 SIT4 PSA1 RPO21 TFP1 YRB1 DBF4 ADR1 SWA2 MRPL35 HXT7 SLF1 GCN4 CUP5 MCM3 CIN8 MNN1 RPN3 ALD5 KAP123 BUR6 PAB1 CCA1 LOC1 ERG26 PMC1 PMA1 CLG1 KIP3 MTO1 PSD2 ATF2 AMA1 PFK1 PUP2 PRS3 RIM4 GPA1 CIC1 SSF1 PCL5 KSP1 SNP1 SDS3 FKH1 PAN1 APS3 RPS22A ANB1 CYC1 VPS25 URA8 SPC42 SMY1 SLD2 CTK1 PTR2 BAS1 YKR106W VPS13 RPL8B POM34 PSR2 YLR179C SAM1 YEF3 YCS4 YSH1 FKS1 IMD3 RRN11 GTR1 MVP1 MSN2 MCM1 TIF34 CTL1 RGM1 PFK2 SKY1 GOT1 FET4 DBP2 AAH1 RPC34 PHO91 MAS6 TOP1 YAP7 PRE6 YOR051C DCI1 WTM2 VPH1 RPA190 TYE7 CIN1 RPS9A RLM1 RPL5 CDC60 GUP2 AFT2 CIT3 HAA1 YOP1 GLN1 VMA13 MRL1 RPL11A PRE2 NCE102 121 3106 hydrogen-translocating V-type ATPase complex [GO:0016471] 0.00135467 TFP1 CUP5 VPH1 VMA13 4 16 intracellular [GO:0005622] 0.00175587 MAK16 CYC3 SAS3 YBR077C UBC4 RFC5 VID24 APE3 CTP1 GPR1 SIT4 PSA1 RPO21 TFP1 YRB1 DBF4 ADR1 SWA2 MRPL35 HXT7 SLF1 GCN4 CUP5 MCM3 CIN8 MNN1 RPN3 ALD5 KAP123 BUR6 PAB1 CCA1 LOC1 ERG26 PMC1 PMA1 CLG1 KIP3 MTO1 PSD2 ATF2 AMA1 PFK1 PUP2 PRS3 RIM4 GPA1 CIC1 SSF1 PCL5 KSP1 SNP1 SDS3 FKH1 PAN1 APS3 RPS22A ANB1 CYC1 VPS25 URA8 SPC42 SLD2 CTK1 PTR2 BAS1 RPL8B POM34 PSR2 YLR179C SAM1 YEF3 YCS4 YSH1 FKS1 IMD3 RRN11 GTR1 MVP1 MSN2 MCM1 TIF34 CTL1 RGM1 PFK2 SKY1 GOT1 FET4 AAH1 RPC34 MAS6 TOP1 YAP7 PRE6 YOR051C DCI1 WTM2 VPH1 RPA190 TYE7 CIN1 RPS9A RLM1 RPL5 CDC60 AFT2 CIT3 HAA1 GLN1 VMA13 MRL1 RPL11A PRE2 NCE102 114 2921 26S proteasome [GO:0005837] 0.00251429 UBC4 RPN3 PUP2 CIC1 PRE6 PRE2 6 44 vacuolar membrane [GO:0005774] 0.00353338 TFP1 CUP5 PMC1 PSD2 VPH1 VMA13 6 47 SMART Domains Category p-value In Category from Cluster k f KISc 0.000596423 CIN8 KIP3 SMY1 3 6 RPOLA_N 0.0029765 RPO21 RPA190 2 3 PFam-A Domains Category p-value In Category from Cluster k f PF00225 (kinesin) 0.000596423 CIN8 KIP3 SMY1 3 6 PF00365 (PFK) 0.00101352 PFK1 PFK2 2 2 PF00096 (zf-C2H2) 0.00196986 SAS3 GIS1 ADR1 MSN2 RGM1 YPR022C 6 42 PF01161 (PBP) 0.0029765 MRPL35 YLR179C 2 3 PF01854 (RNA_pol_A2) 0.0029765 RPO21 RPA190 2 3 PF00623 (RNA_pol_A) 0.0029765 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 Yeast Two Hybrid - Ito (full) Category p-value In Category from Cluster k f YKR007W 0.0029765 YBR077C GTR1 2 3 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 YPR110C (RPC40) 0.000835138 TFP1 AHA1 ADR1 RPN3 RPC34 RPA190 CDC60 7 49 Cellzome Complexes Category p-value In Category from Cluster k f YMR205C (PFK2) 0.00101352 PFK1 PFK2 2 2 YBR207W (FTH1) 0.00101923 RPN3 KAP123 FKS1 3 7 YGR020C (VMA7) 0.00159254 TFP1 VPH1 VMA13 3 8 Proteome Localization--Observed Category p-value In Category from Cluster k f 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- 0.0041219 MAK16 LOC1 CIC1 RPS22A RPL5 5 34