Input Cluster (n=194) YAL035W FUN12 YAL036C FUN11 YAR035W YAT1 YBL027W RPL19B YBL028C YBL054W YBL055C YBR029C CDS1 YBR030W YBR107C IML3 YBR122C MRPL36 YBR141C YBR142W MAK5 YBR148W YSW1 YBR260C RGD1 YBR267W YCR016W YCR021C HSP30 YCR054C CTR86 YDL042C SIR2 YDL051W LHP1 YDL052C SLC1 YDL063C YDL112W TRM3 YDL113C CVT20 YDL115C IWR1 YDL182W LYS20 YDR101C ARX1 YDR123C INO2 YDR240C SNU56 YDR262W YDR299W BFR2 YDR320C SWA2 YDR321W ASP1 YDR329C PEX3 YDR365C YDR384C ATO3 YDR441C APT2 YDR465C RMT2 YDR466W YEL036C ANP1 YEL065W SIT1 YER073W ALD5 YER075C PTP3 YER104W RTT105 YER114C BOI2 YER126C NSA2 YER127W LCP5 YER138W-A YER151C UBP3 YER168C CCA1 YFR017C YFR037C RSC8 YGL009C LEU1 YGL055W OLE1 YGL057C YGL071W RCS1 YGL209W MIG2 YGL255W ZRT1 YGR030C POP6 YGR057C LST7 YGR058W YGR067C YGR078C PAC10 YGR102C YGR103W NOP7 YGR126W YGR128C UTP8 YGR129W SYF2 YGR145W ENP2 YGR162W TIF4631 YGR172C YIP1 YGR210C YGR211W ZPR1 YGR246C BRF1 YGR276C RNH70 YGR285C ZUO1 YHL017W YHL019C APM2 YHR065C RRP3 YHR066W SSF1 YHR206W SKN7 YIL019W YIL026C IRR1 YIL046W MET30 YIL047C SYG1 YIL078W THS1 YIL079C AIR1 YIL083C YIL084C SDS3 YIL090W YIL091C YIR014W YIR027C DAL1 YJL033W HCA4 YJL083W YJL112W MDV1 YJR055W HIT1 YJR104C SOD1 YJR105W ADO1 YKL029C MAE1 YKL078W DHR2 YKL081W TEF4 YKL082C YKL098W YKL099C UTP11 YKL150W MCR1 YKL151C YKL187C YKR013W PRY2 YKR024C DBP7 YKR025W RPC37 YLL022C HIF1 YLL048C YBT1 YLR004C YLR005W SSL1 YLR055C SPT8 YLR056W ERG3 YLR071C RGR1 YLR168C YLR214W FRE1 YLR237W THI7 YLR276C DBP9 YLR373C VID22 YLR380W CSR1 YLR401C YLR411W CTR3 YML006C GIS4 YML034W SRC1 YML035C AMD1 YML038C YMD8 YML043C RRN11 YML123C PHO84 YML126C ERG13 YMR014W BUD22 YMR131C RRB1 YMR185W YMR246W FAA4 YMR259C YMR290C HAS1 YMR292W GOT1 YMR302C PRP12 YNL061W NOP2 YNL062C GCD10 YNL095C YNL110C NOP15 YNL115C YNL119W YNL121C TOM70 YNL132W KRE33 YNL133C FYV6 YNL141W AAH1 YNL299W TRF5 YNR003C RPC34 YNR011C PRP2 YNR012W URK1 YOL010W RCL1 YOL053W YOL060C MAM3 YOL075C YOL076W MDM20 YOL077C BRX1 YOL109W YOL125W YOL141W PPM2 YOR004W YOR048C RAT1 YOR056C NOB1 YOR057W SGT1 YOR095C RKI1 YOR236W DFR1 YOR265W RBL2 YOR272W YTM1 YOR294W RRS1 YOR302W YPL012W RRP12 YPL013C YPL023C MET12 YPL040C ISM1 YPL081W RPS9A YPL099C YPL101W ELP4 YPL126W NAN1 YPL127C HHO1 YPL149W APG5 YPL245W YPL246C YPL278C YPR001W CIT3 YPR010C RPA135 YPR091C YPR112C MRD1 YPR113W PIS1 YPR144C UTP19 Genes Not Found: YAR009C YAR010C YER138C YFL002W-A YJR028W YJR029W MIPS Functional Classification Category p-value In Category from Cluster k f rRNA transcription 1.05104e-06 MAK5 LCP5 POP6 BRF1 RRP3 HCA4 DBP7 RRN11 RRB1 PRP12 NOP2 RPC34 RAT1 RRS1 RPA135 15 109 other rRNA-transcription activities 0.000545283 RRB1 PRP12 RRS1 3 6 TRANSCRIPTION 0.000583652 YBL054W MAK5 SIR2 LHP1 TRM3 INO2 SNU56 LCP5 UBP3 CCA1 RSC8 RCS1 MIG2 POP6 YGR067C SYF2 BRF1 RRP3 SKN7 MET30 SDS3 HCA4 DHR2 DBP7 RPC37 SSL1 SPT8 RGR1 RRN11 RRB1 PRP12 NOP2 GCD10 RPC34 PRP2 RCL1 RAT1 RRS1 ELP4 RPA135 40 771 rRNA processing 0.00065607 MAK5 LCP5 POP6 RRP3 HCA4 DBP7 NOP2 RAT1 8 63 purine ribonucleotide metabolism 0.00242481 APT2 DAL1 ADO1 AMD1 AAH1 DFR1 6 45 lipid and fatty-acid transport 0.00352303 YAT1 YBT1 CSR1 FAA4 4 21 MIPS Phenotypes Category p-value In Category from Cluster k f MIPS Subcellular Localization Category p-value In Category from Cluster k f nucleolus 1.80946e-05 SIR2 LCP5 POP6 RRP3 SSF1 RRB1 NOP2 RCL1 NAN1 9 50 MIPS Protein Complexes Category p-value In Category from Cluster k f MIPS Protein Classes Category p-value In Category from Cluster k f GO Molecular Function Category p-value In Category from Cluster k f RNA helicase [GO:0003724] 1.96864e-05 MAK5 RRP3 HCA4 DHR2 DBP7 DBP9 HAS1 PRP2 8 39 ATP dependent RNA helicase [GO:0004004] 8.82051e-05 MAK5 RRP3 HCA4 DBP7 DBP9 PRP2 6 25 RNA dependent adenosinetriphosphatase [GO:0008186] 8.82051e-05 MAK5 RRP3 HCA4 DBP7 DBP9 PRP2 6 25 ATP dependent helicase [GO:0008026] 0.000624601 MAK5 RRP3 HCA4 DBP7 DBP9 PRP2 6 35 RNA binding [GO:0003723] 0.000783019 MAK5 LHP1 SNU56 LCP5 POP6 UTP8 RNH70 RRP3 HCA4 DHR2 UTP11 DBP7 DBP9 HAS1 PRP2 RAT1 NAN1 MRD1 18 253 helicase [GO:0004386] 0.00109744 MAK5 RRP3 HCA4 DHR2 DBP7 DBP9 HAS1 PRP2 8 68 nucleoside kinase [GO:0019206] 0.00280198 ADO1 URK1 2 3 GO Biological Process Category p-value In Category from Cluster k f ribosome biogenesis [GO:0007046] 3.63565e-12 MAK5 NSA2 LCP5 POP6 NOP7 UTP8 RRP3 HCA4 DHR2 UTP11 DBP7 DBP9 RRB1 PRP12 NOP2 NOP15 RCL1 RAT1 YTM1 RRS1 RRP12 NAN1 MRD1 23 127 ribosome biogenesis and assembly [GO:0042254] 2.43034e-11 MAK5 NSA2 LCP5 POP6 NOP7 UTP8 RRP3 SSF1 HCA4 DHR2 UTP11 DBP7 DBP9 RRB1 PRP12 NOP2 NOP15 RCL1 BRX1 RAT1 YTM1 RRS1 RRP12 NAN1 MRD1 25 165 rRNA processing [GO:0006364] 5.24973e-08 MAK5 LCP5 POP6 UTP8 RRP3 HCA4 UTP11 DBP7 DBP9 PRP12 NOP2 RCL1 RAT1 RRP12 NAN1 MRD1 16 100 transcription from Pol I promoter [GO:0006360] 8.54078e-08 MAK5 LCP5 POP6 UTP8 RRP3 HCA4 UTP11 DBP7 DBP9 RRN11 PRP12 NOP2 RCL1 RAT1 RRP12 NAN1 RPA135 MRD1 18 131 RNA processing [GO:0006396] 1.11617e-06 MAK5 LHP1 TRM3 SNU56 LCP5 CCA1 POP6 UTP8 SYF2 RNH70 RRP3 HCA4 UTP11 DBP7 DBP9 YLR401C PRP12 NOP2 GCD10 PRP2 RCL1 RAT1 RRP12 NAN1 MRD1 25 277 RNA metabolism [GO:0016070] 9.09906e-06 MAK5 LHP1 TRM3 SNU56 LCP5 CCA1 POP6 UTP8 SYF2 RNH70 RRP3 HCA4 UTP11 DBP7 DBP9 YLR401C PRP12 NOP2 GCD10 PRP2 RCL1 RAT1 RRP12 NAN1 MRD1 25 311 cytoplasm organization and biogenesis [GO:0007028] 1.14109e-05 MAK5 CVT20 SWA2 PEX3 BOI2 NSA2 LCP5 OLE1 POP6 PAC10 NOP7 UTP8 RRP3 SSF1 HCA4 MDV1 DHR2 UTP11 DBP7 DBP9 VID22 BUD22 RRB1 GOT1 PRP12 NOP2 NOP15 TOM70 RCL1 MAM3 MDM20 BRX1 RAT1 RBL2 YTM1 RRS1 RRP12 NAN1 APG5 MRD1 40 646 transcription, DNA-dependent [GO:0006351] 2.30339e-05 MAK5 SIR2 INO2 PTP3 LCP5 RCS1 MIG2 POP6 UTP8 BRF1 RRP3 SDS3 HCA4 UTP11 DBP7 RPC37 SSL1 RGR1 DBP9 RRN11 PRP12 NOP2 RPC34 RCL1 RAT1 RRP12 ELP4 NAN1 HHO1 RPA135 MRD1 31 457 transcription [GO:0006350] 2.36886e-05 MAK5 SIR2 INO2 PTP3 LCP5 RCS1 MIG2 POP6 UTP8 BRF1 RRP3 SKN7 SDS3 HCA4 UTP11 DBP7 RPC37 SSL1 RGR1 DBP9 RRN11 PRP12 NOP2 RPC34 RCL1 RAT1 RRP12 ELP4 NAN1 HHO1 RPA135 MRD1 32 480 ribosomal large subunit biogenesis [GO:0042273] 0.000511096 NSA2 NOP7 NOP15 YTM1 4 13 cell organization and biogenesis [GO:0016043] 0.000748722 MAK5 SIR2 CVT20 SWA2 PEX3 BOI2 NSA2 LCP5 RSC8 OLE1 POP6 PAC10 NOP7 UTP8 RRP3 SSF1 SDS3 HCA4 MDV1 DHR2 UTP11 DBP7 SPT8 DBP9 VID22 CSR1 AMD1 BUD22 RRB1 GOT1 PRP12 NOP2 NOP15 TOM70 RCL1 MAM3 MDM20 BRX1 RAT1 RBL2 YTM1 RRS1 RRP12 NAN1 APG5 MRD1 46 939 35S primary transcript processing [GO:0006365] 0.002156 LCP5 RRP3 HCA4 DBP7 DBP9 MRD1 6 44 nucleobase, nucleoside, nucleotide and nucleic acid metabolism [GO:0006139] 0.00234056 MAK5 SIR2 LHP1 TRM3 INO2 SNU56 PTP3 RTT105 LCP5 CCA1 RSC8 RCS1 MIG2 POP6 UTP8 SYF2 BRF1 RNH70 RRP3 SKN7 AIR1 SDS3 HCA4 ADO1 UTP11 DBP7 RPC37 SSL1 SPT8 RGR1 DBP9 YLR401C RRN11 PRP12 NOP2 GCD10 AAH1 RPC34 PRP2 URK1 RCL1 RAT1 RRP12 ELP4 NAN1 HHO1 RPA135 MRD1 48 1046 ribosomal large subunit assembly and maintenance [GO:0000027] 0.00411599 MAK5 SSF1 DBP7 DBP9 BRX1 5 35 tRNA metabolism [GO:0006399] 0.00420312 TRM3 CCA1 YLR401C GCD10 4 22 tRNA modification [GO:0006400] 0.00420312 TRM3 CCA1 YLR401C GCD10 4 22 GO Cellular Component Category p-value In Category from Cluster k f nucleolus [GO:0005730] 1.2903e-12 SIR2 LCP5 POP6 NOP7 UTP8 ZPR1 RRP3 SSF1 HCA4 DHR2 UTP11 DBP7 DBP9 RRN11 RRB1 HAS1 NOP2 NOP15 RCL1 BRX1 YTM1 NAN1 RPA135 MRD1 24 133 nucleus [GO:0005634] 8.16425e-06 MAK5 SIR2 LHP1 LYS20 INO2 SNU56 NSA2 LCP5 CCA1 RSC8 RCS1 MIG2 POP6 NOP7 UTP8 SYF2 ZPR1 BRF1 RRP3 SSF1 SKN7 IRR1 MET30 AIR1 SDS3 HCA4 DHR2 UTP11 DBP7 RPC37 SSL1 SPT8 RGR1 DBP9 RRN11 BUD22 RRB1 HAS1 NOP2 GCD10 NOP15 TRF5 RPC34 PRP2 RCL1 BRX1 RAT1 YTM1 RRS1 ELP4 NAN1 HHO1 RPA135 MRD1 UTP19 55 1007 cell [GO:0005623] 0.00233142 FUN12 YAT1 RPL19B CDS1 MRPL36 MAK5 RGD1 HSP30 SIR2 LHP1 SLC1 CVT20 LYS20 INO2 SNU56 SWA2 ASP1 PEX3 ANP1 SIT1 ALD5 PTP3 BOI2 NSA2 LCP5 UBP3 CCA1 RSC8 LEU1 OLE1 RCS1 MIG2 ZRT1 POP6 LST7 PAC10 NOP7 UTP8 SYF2 TIF4631 YIP1 ZPR1 BRF1 RNH70 ZUO1 APM2 RRP3 SSF1 SKN7 IRR1 MET30 SYG1 THS1 AIR1 SDS3 DAL1 HCA4 MDV1 SOD1 MAE1 DHR2 TEF4 UTP11 MCR1 DBP7 RPC37 YBT1 SSL1 SPT8 ERG3 RGR1 FRE1 THI7 DBP9 VID22 CTR3 RRN11 PHO84 ERG13 BUD22 RRB1 FAA4 HAS1 GOT1 PRP12 NOP2 GCD10 NOP15 TOM70 AAH1 TRF5 RPC34 PRP2 RCL1 YOL075C MDM20 BRX1 RAT1 NOB1 SGT1 DFR1 RBL2 YTM1 RRS1 RRP12 MET12 ISM1 RPS9A ELP4 NAN1 HHO1 CIT3 RPA135 MRD1 PIS1 UTP19 116 3106 intracellular [GO:0005622] 0.00414291 FUN12 YAT1 RPL19B CDS1 MRPL36 MAK5 RGD1 HSP30 SIR2 LHP1 SLC1 LYS20 INO2 SNU56 SWA2 PEX3 ANP1 SIT1 ALD5 PTP3 NSA2 LCP5 UBP3 CCA1 RSC8 OLE1 RCS1 MIG2 ZRT1 POP6 LST7 PAC10 NOP7 UTP8 SYF2 TIF4631 YIP1 ZPR1 BRF1 ZUO1 APM2 RRP3 SSF1 SKN7 IRR1 MET30 SYG1 THS1 AIR1 SDS3 DAL1 HCA4 MDV1 SOD1 MAE1 DHR2 TEF4 UTP11 MCR1 DBP7 RPC37 YBT1 SSL1 SPT8 ERG3 RGR1 FRE1 THI7 DBP9 VID22 CTR3 RRN11 PHO84 ERG13 BUD22 RRB1 FAA4 HAS1 GOT1 PRP12 NOP2 GCD10 NOP15 TOM70 AAH1 TRF5 RPC34 PRP2 RCL1 MDM20 BRX1 RAT1 NOB1 SGT1 DFR1 RBL2 YTM1 RRS1 RRP12 ISM1 RPS9A ELP4 NAN1 HHO1 CIT3 RPA135 MRD1 PIS1 UTP19 109 2921 SMART Domains Category p-value In Category from Cluster k f COIL 7.72372e-05 FUN12 RPL19B YBL028C YBR030W YSW1 RGD1 YBR267W CVT20 ARX1 BFR2 YDR365C ANP1 BOI2 LCP5 UBP3 RSC8 OLE1 NOP7 ENP2 TIF4631 RNH70 ZUO1 RRP3 SSF1 SKN7 YIL019W THS1 HCA4 MDV1 YKL082C DBP9 SRC1 BUD22 NOP2 YNL119W KRE33 BRX1 YOL109W RAT1 NOB1 RBL2 YPL099C MRD1 43 776 HELICc 0.00246492 MAK5 RRP3 HCA4 DHR2 DBP7 DBP9 HAS1 PRP2 8 77 DEXDc 0.0031383 MAK5 RRP3 HCA4 DHR2 DBP7 DBP9 HAS1 PRP2 8 80 PFam-A Domains Category p-value In Category from Cluster k f PF00271 (helicase_C) 0.00246492 MAK5 RRP3 HCA4 DHR2 DBP7 DBP9 HAS1 PRP2 8 77 PF02824 (TGS) 0.00280198 FUN11 THS1 2 3 PF00270 (DEAD) 0.00459944 MAK5 RRP3 HCA4 DBP7 DBP9 HAS1 6 51 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 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 YDL213C (FYV14) 2.51849e-05 NOP7 ENP2 TIF4631 DBP7 HAS1 NOP2 KRE33 YTM1 RRP12 9 52 YIL035C (CKA1) 0.000110654 NOP7 ENP2 TIF4631 SSF1 YKL082C HAS1 NOP2 KRE33 8 49 YER082C (UTP7) 0.000366617 TIF4631 KRE33 BRX1 RRP12 NAN1 5 21 YLR427W 0.000865481 FUN12 TIF4631 HAS1 KRE33 RRP12 5 25 YOR005C (DNL4) 0.000929352 NOP7 NOP2 NOP15 YTM1 4 15 YMR049C (ERB1) 0.000983463 NOP7 HAS1 NOP2 NOP15 BRX1 YTM1 6 38 YPR017C (DSS4) 0.0014581 ARX1 NOP7 FAA4 3 8 YNL061W (NOP2) 0.00154354 NSA2 NOP7 PHO84 BRX1 4 17 YLR074C (BUD20) 0.00191031 LHP1 ARX1 NSA2 NOP7 TEF4 YPL013C 6 43 YHR052W (CIC1) 0.0021375 MAK5 NOP2 KRE33 3 9 YDL047W (SIT4) 0.00496663 RMT2 ADO1 MAE1 FAA4 4 23 Cellzome Complexes Category p-value In Category from Cluster k f YPL043W (NOP4) 3.50918e-07 NOP7 DBP9 HAS1 NOP2 KRE33 BRX1 YTM1 RRP12 8 24 YDR060W (MAK21) 5.0247e-07 MAK5 NOP7 DBP9 HAS1 NOP15 BRX1 YTM1 RRP12 8 25 YNL110C (NOP15) 7.06686e-07 ARX1 NSA2 NOP7 HAS1 NOP15 BRX1 YTM1 RRP12 8 26 YMR049C (ERB1) 5.99785e-06 NOP7 HAS1 NOP2 NOP15 BRX1 5 10 YGL099W (LSG1) 4.01612e-05 YBR267W ARX1 BFR2 LCP5 KRE33 NAN1 6 22 YHR066W (SSF1) 6.87925e-05 MAK5 NOP7 SSF1 DBP9 HAS1 NOP2 6 24 YCR057C (PWP2) 0.000114347 YDR365C UTP8 ENP2 UTP11 KRE33 NAN1 UTP19 7 37 YLR074C (BUD20) 0.000220341 LHP1 ARX1 NSA2 NOP7 NOP15 5 19 YGR090W (UTP22) 0.000286464 UTP8 ENP2 NOP2 NAN1 UTP19 5 20 YLR175W (CBF5) 0.00036257 FUN12 TIF4631 HAS1 RRP12 4 12 YBR247C (ENP1) 0.00104494 KRE33 RCL1 NOB1 RRP12 UTP19 5 26 YKR081C (RPF2) 0.00120937 ARX1 NOP7 NOP15 YTM1 4 16 YBR142W (MAK5) 0.00193697 MAK5 HAS1 NOP2 YTM1 4 18 YER082C (UTP7) 0.00239474 UTP8 KRE33 NAN1 MRD1 4 19 YBR267W 0.00280198 YBR267W ARX1 2 3 Proteome Localization--Observed Category p-value In Category from Cluster k f nucleus 0.000110602 YBL028C YBL054W SIR2 YDL063C LYS20 ARX1 YDR365C LCP5 RSC8 NOP7 SYF2 ENP2 SKN7 SDS3 PRY2 SSL1 SPT8 BUD22 HAS1 NOP2 NOP15 YOL125W YOR004W NOB1 RKI1 DFR1 YTM1 NAN1 HHO1 29 450 Proteome Localization--Predicted+Observed Category p-value In Category from Cluster k f nuc 0.00070651 YBL028C YBL054W CDS1 MAK5 YSW1 SIR2 YDL063C CVT20 ARX1 SNU56 BFR2 YDR365C YDR466W LCP5 RSC8 RCS1 MIG2 POP6 YGR058W YGR067C YGR102C NOP7 UTP8 SYF2 ENP2 YIP1 BRF1 ZUO1 RRP3 SSF1 SKN7 YIL019W MET30 AIR1 SDS3 YIL091C HCA4 DHR2 YKL098W PRY2 DBP7 SSL1 SPT8 RGR1 DBP9 VID22 RRN11 BUD22 HAS1 NOP2 NOP15 KRE33 RPC34 PRP2 YOL125W YOR004W RAT1 NOB1 YTM1 NAN1 HHO1 APG5 YPL278C RPA135 64 1435 Deletions Consortium (Essentiality, Morphology) Category p-value In Category from Cluster k f essential 1.24148e-06 CDS1 MAK5 CTR86 SNU56 BFR2 YDR365C RTT105 NSA2 LCP5 CCA1 RSC8 OLE1 POP6 NOP7 UTP8 ENP2 YIP1 ZPR1 BRF1 RRP3 YIL019W IRR1 MET30 THS1 YIL083C YIL091C HCA4 DHR2 YKL082C UTP11 RPC37 SSL1 RGR1 DBP9 RRN11 ERG13 RRB1 YMR185W HAS1 NOP2 GCD10 NOP15 KRE33 RPC34 PRP2 RCL1 BRX1 YOR004W RAT1 NOB1 SGT1 RKI1 DFR1 YTM1 RRS1 RRP12 NAN1 RPA135 MRD1 PIS1 UTP19 61 1101 Morphology - neck abnormalities 0.000953474 SWA2 MDM20 2 2 Yeast Fitness Data Category p-value In Category from Cluster k f Published Complexes Category p-value In Category from Cluster k f Andersen et al. (2002) - Curr Bio 12:1- 2.79636e-06 BFR2 NSA2 NOP7 ENP2 RRP3 SSF1 YIL091C HCA4 UTP11 DBP9 HAS1 NOP2 KRE33 RCL1 YTM1 RRS1 RRP12 MRD1 18 165 Harnicharnpai et al. (2001) - Mol Cell 8:505- 0.00053102 NSA2 NOP7 HAS1 NOP15 BRX1 YTM1 6 34 Bassler et al. (2001) - Mol Cell 8:517- 0.00125061 ARX1 NSA2 NOP7 HAS1 NOP2 5 27