Input Cluster (n=193) YAL035W FUN12 YAL036C FUN11 YAR020C PAU7 YAR035W YAT1 YBL027W RPL19B YBL028C YBL054W YBL055C YBR029C CDS1 YBR030W YBR107C IML3 YBR122C MRPL36 YBR142W MAK5 YBR155W CNS1 YBR260C RGD1 YBR267W YCR021C HSP30 YCR054C CTR86 YDL051W LHP1 YDL052C SLC1 YDL063C YDL113C CVT20 YDL115C IWR1 YDL182W LYS20 YDR101C ARX1 YDR123C INO2 YDR262W YDR299W BFR2 YDR320C SWA2 YDR321W ASP1 YDR329C PEX3 YDR365C YDR384C ATO3 YDR406W PDR15 YDR441C APT2 YDR449C UTP6 YDR465C RMT2 YDR466W YDR508C GNP1 YEL036C ANP1 YEL065W SIT1 YER073W ALD5 YER075C PTP3 YER104W RTT105 YER126C NSA2 YER127W LCP5 YER138W-A YER140W YER151C UBP3 YER152C YER168C CCA1 YFL003C MSH4 YFR017C YFR037C RSC8 YGL009C LEU1 YGL055W OLE1 YGL057C YGL209W MIG2 YGL235W YGL251C HFM1 YGL255W ZRT1 YGR057C LST7 YGR058W YGR067C YGR078C PAC10 YGR102C YGR103W NOP7 YGR126W YGR128C UTP8 YGR129W SYF2 YGR145W ENP2 YGR162W TIF4631 YGR172C YIP1 YGR210C YGR211W ZPR1 YGR285C ZUO1 YHL017W YHL019C APM2 YHR065C RRP3 YHR066W SSF1 YHR206W SKN7 YIL019W YIL026C IRR1 YIL046W MET30 YIL047C SYG1 YIL078W THS1 YIL079C AIR1 YIL083C YIL090W YIL091C YIL165C YIR014W YIR027C DAL1 YJL019W MPS3 YJL020C BBC1 YJL033W HCA4 YJL083W YJL210W PEX2 YJR055W HIT1 YJR104C SOD1 YJR105W ADO1 YKL029C MAE1 YKL033W YKL078W DHR2 YKL081W TEF4 YKL082C YKL098W YKL099C UTP11 YKL150W MCR1 YKL151C YKL187C YKR013W PRY2 YKR063C LAS1 YLL048C YBT1 YLR004C YLR005W SSL1 YLR055C SPT8 YLR071C RGR1 YLR168C YLR214W FRE1 YLR222C UTP13 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 YMR292W GOT1 YMR302C PRP12 YNL061W NOP2 YNL062C GCD10 YNL095C YNL110C NOP15 YNL115C YNL119W YNL121C TOM70 YNL132W KRE33 YNL133C FYV6 YNL141W AAH1 YNL299W TRF5 YNR011C PRP2 YNR012W URK1 YOL010W RCL1 YOL053W YOL059W GPD2 YOL060C MAM3 YOL075C YOL076W MDM20 YOL077C BRX1 YOL109W YOL125W YOL141W PPM2 YOR001W RRP6 YOR004W YOR048C RAT1 YOR056C NOB1 YOR057W SGT1 YOR116C RPO31 YOR119C RIO1 YOR142W LSC1 YOR236W DFR1 YOR265W RBL2 YOR272W YTM1 YOR302W YPL012W RRP12 YPL013C YPL023C MET12 YPL040C ISM1 YPL099C YPL101W ELP4 YPL126W NAN1 YPL127C HHO1 YPL149W APG5 YPL246C YPL278C YPR001W CIT3 YPR010C RPA135 YPR091C YPR112C MRD1 YPR113W PIS1 YPR144C UTP19 Genes Not Found: YAR009C YAR010C YER138C YFL002W-A YJR028W YJR029W YLR035C-A MIPS Functional Classification Category p-value In Category from Cluster k f rRNA transcription 0.000488602 MAK5 LCP5 RRP3 HCA4 RRN11 RRB1 PRP12 NOP2 RAT1 RPO31 RPA135 11 109 purine ribonucleotide metabolism 0.00236246 APT2 DAL1 ADO1 AMD1 AAH1 DFR1 6 45 lipid and fatty-acid transport 0.00345795 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 0.000765592 LCP5 RRP3 SSF1 RRB1 NOP2 RCL1 NAN1 7 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 snoRNA binding [GO:0030515] 0.00020742 UTP6 UTP8 UTP11 UTP13 NAN1 MRD1 6 29 ATP dependent RNA helicase [GO:0004004] 0.000845448 MAK5 RRP3 HCA4 DBP9 PRP2 5 25 RNA dependent adenosinetriphosphatase [GO:0008186] 0.000845448 MAK5 RRP3 HCA4 DBP9 PRP2 5 25 RNA helicase [GO:0003724] 0.00110278 MAK5 RRP3 HCA4 DHR2 DBP9 PRP2 6 39 nucleoside kinase [GO:0019206] 0.0027734 ADO1 URK1 2 3 ATP dependent helicase [GO:0008026] 0.004026 MAK5 RRP3 HCA4 DBP9 PRP2 5 35 helicase [GO:0004386] 0.00466439 MAK5 HFM1 RRP3 HCA4 DHR2 DBP9 PRP2 7 68 RNA binding [GO:0003723] 0.00475629 MAK5 LHP1 UTP6 LCP5 UTP8 RRP3 HCA4 DHR2 UTP11 UTP13 DBP9 PRP2 RRP6 RAT1 NAN1 MRD1 16 253 GO Biological Process Category p-value In Category from Cluster k f ribosome biogenesis [GO:0007046] 3.9746e-13 MAK5 UTP6 NSA2 LCP5 NOP7 UTP8 RRP3 HCA4 DHR2 UTP11 UTP13 DBP9 RRB1 PRP12 NOP2 NOP15 RCL1 RRP6 RAT1 RIO1 YTM1 RRP12 NAN1 MRD1 24 127 ribosome biogenesis and assembly [GO:0042254] 3.26938e-12 MAK5 UTP6 NSA2 LCP5 NOP7 UTP8 RRP3 SSF1 HCA4 DHR2 UTP11 UTP13 DBP9 RRB1 PRP12 NOP2 NOP15 RCL1 BRX1 RRP6 RAT1 RIO1 YTM1 RRP12 NAN1 MRD1 26 165 rRNA processing [GO:0006364] 9.43394e-10 MAK5 UTP6 LCP5 UTP8 RRP3 HCA4 UTP11 UTP13 DBP9 PRP12 NOP2 RCL1 RRP6 RAT1 RIO1 RRP12 NAN1 MRD1 18 100 transcription from Pol I promoter [GO:0006360] 2.19488e-09 MAK5 UTP6 LCP5 UTP8 RRP3 HCA4 UTP11 UTP13 DBP9 RRN11 PRP12 NOP2 RCL1 RRP6 RAT1 RIO1 RRP12 NAN1 RPA135 MRD1 20 131 RNA processing [GO:0006396] 3.51033e-06 MAK5 LHP1 UTP6 LCP5 CCA1 UTP8 SYF2 RRP3 HCA4 UTP11 UTP13 DBP9 YLR401C PRP12 NOP2 GCD10 PRP2 RCL1 RRP6 RAT1 RIO1 RRP12 NAN1 MRD1 24 277 cytoplasm organization and biogenesis [GO:0007028] 4.05729e-06 MAK5 CVT20 SWA2 PEX3 UTP6 NSA2 LCP5 OLE1 PAC10 NOP7 UTP8 RRP3 SSF1 HCA4 PEX2 DHR2 UTP11 LAS1 UTP13 DBP9 VID22 BUD22 RRB1 GOT1 PRP12 NOP2 NOP15 TOM70 RCL1 MAM3 MDM20 BRX1 RRP6 RAT1 RIO1 RBL2 YTM1 RRP12 NAN1 APG5 MRD1 41 646 RNA metabolism [GO:0016070] 2.53009e-05 MAK5 LHP1 UTP6 LCP5 CCA1 UTP8 SYF2 RRP3 HCA4 UTP11 UTP13 DBP9 YLR401C PRP12 NOP2 GCD10 PRP2 RCL1 RRP6 RAT1 RIO1 RRP12 NAN1 MRD1 24 311 processing of 20S pre-rRNA [GO:0030490] 2.62801e-05 UTP6 UTP8 UTP11 UTP13 RIO1 RRP12 NAN1 7 30 transcription [GO:0006350] 0.000308584 MAK5 INO2 UTP6 PTP3 LCP5 MIG2 UTP8 RRP3 SKN7 HCA4 UTP11 SSL1 RGR1 UTP13 DBP9 RRN11 PRP12 NOP2 RCL1 RRP6 RAT1 RPO31 RIO1 RRP12 ELP4 NAN1 HHO1 RPA135 MRD1 29 480 transcription, DNA-dependent [GO:0006351] 0.000314746 MAK5 INO2 UTP6 PTP3 LCP5 MIG2 UTP8 RRP3 HCA4 UTP11 SSL1 RGR1 UTP13 DBP9 RRN11 PRP12 NOP2 RCL1 RRP6 RAT1 RPO31 RIO1 RRP12 ELP4 NAN1 HHO1 RPA135 MRD1 28 457 ribosomal large subunit biogenesis [GO:0042273] 0.000501144 NSA2 NOP7 NOP15 YTM1 4 13 cell organization and biogenesis [GO:0016043] 0.00123534 MAK5 CVT20 SWA2 PEX3 UTP6 NSA2 LCP5 RSC8 OLE1 PAC10 NOP7 UTP8 RRP3 SSF1 HCA4 PEX2 DHR2 UTP11 LAS1 SPT8 UTP13 DBP9 VID22 CSR1 AMD1 BUD22 RRB1 GOT1 PRP12 NOP2 NOP15 TOM70 RCL1 MAM3 MDM20 BRX1 RRP6 RAT1 RIO1 RBL2 YTM1 RRP12 NAN1 APG5 MRD1 45 939 35S primary transcript processing [GO:0006365] 0.00210028 LCP5 RRP3 HCA4 DBP9 RRP6 MRD1 6 44 GO Cellular Component Category p-value In Category from Cluster k f nucleolus [GO:0005730] 6.4814e-11 UTP6 LCP5 NOP7 UTP8 ZPR1 RRP3 SSF1 HCA4 DHR2 UTP11 UTP13 DBP9 RRN11 RRB1 NOP2 NOP15 RCL1 BRX1 YTM1 NAN1 RPA135 MRD1 22 133 nucleus [GO:0005634] 0.000131573 MAK5 LHP1 LYS20 INO2 UTP6 NSA2 LCP5 CCA1 MSH4 RSC8 MIG2 HFM1 NOP7 UTP8 SYF2 ZPR1 RRP3 SSF1 SKN7 IRR1 MET30 AIR1 HCA4 DHR2 UTP11 LAS1 SSL1 SPT8 RGR1 UTP13 DBP9 RRN11 BUD22 RRB1 NOP2 GCD10 NOP15 TRF5 PRP2 RCL1 BRX1 RRP6 RAT1 RPO31 YTM1 ELP4 NAN1 HHO1 RPA135 MRD1 UTP19 51 1007 small nucleolar ribonucleoprotein complex [GO:0005732] 0.00020742 UTP6 LCP5 UTP8 UTP11 UTP13 NAN1 6 29 SMART Domains Category p-value In Category from Cluster k f COIL 6.7988e-05 FUN12 RPL19B YBL028C YBR030W CNS1 RGD1 YBR267W CVT20 ARX1 BFR2 YDR365C ANP1 LCP5 UBP3 RSC8 OLE1 NOP7 ENP2 TIF4631 ZUO1 RRP3 SSF1 SKN7 YIL019W THS1 MPS3 BBC1 HCA4 YKL082C UTP13 DBP9 SRC1 BUD22 NOP2 YNL119W KRE33 BRX1 YOL109W RAT1 NOB1 RBL2 YPL099C MRD1 43 776 PFam-A Domains Category p-value In Category from Cluster k f PF02824 (TGS) 0.0027734 FUN11 THS1 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 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 YCR057C (PWP2) 2.87687e-05 UTP6 YGR210C UTP13 3 3 YJL069C (UTP18) 8.57035e-05 UTP6 LCP5 UTP11 UTP13 KRE33 NAN1 6 25 YER082C (UTP7) 0.000357941 TIF4631 KRE33 BRX1 RRP12 NAN1 5 21 YIL035C (CKA1) 0.000675733 NOP7 ENP2 TIF4631 SSF1 YKL082C NOP2 KRE33 7 49 YOR005C (DNL4) 0.000911488 NOP7 NOP2 NOP15 YTM1 4 15 YDL213C (FYV14) 0.000973556 NOP7 ENP2 TIF4631 NOP2 KRE33 YTM1 RRP12 7 52 YPR017C (DSS4) 0.00143643 ARX1 NOP7 FAA4 3 8 YNL061W (NOP2) 0.00151425 NSA2 NOP7 PHO84 BRX1 4 17 YLR074C (BUD20) 0.00186069 LHP1 ARX1 NSA2 NOP7 TEF4 YPL013C 6 43 YHR052W (CIC1) 0.00210598 MAK5 NOP2 KRE33 3 9 YDL047W (SIT4) 0.00487611 RMT2 ADO1 MAE1 FAA4 4 23 Cellzome Complexes Category p-value In Category from Cluster k f YCR057C (PWP2) 1.21925e-06 YDR365C UTP6 UTP8 ENP2 UTP11 UTP13 KRE33 NAN1 UTP19 9 37 YPL043W (NOP4) 5.22791e-06 NOP7 DBP9 NOP2 KRE33 BRX1 YTM1 RRP12 7 24 YDR060W (MAK21) 7.07318e-06 MAK5 NOP7 DBP9 NOP15 BRX1 YTM1 RRP12 7 25 YNL110C (NOP15) 9.42882e-06 ARX1 NSA2 NOP7 NOP15 BRX1 YTM1 RRP12 7 26 YER082C (UTP7) 1.53244e-05 UTP6 UTP8 UTP13 KRE33 NAN1 MRD1 6 19 YGR090W (UTP22) 2.13346e-05 UTP6 UTP8 ENP2 NOP2 NAN1 UTP19 6 20 YGL099W (LSG1) 3.9006e-05 YBR267W ARX1 BFR2 LCP5 KRE33 NAN1 6 22 YBR247C (ENP1) 0.000108586 UTP6 KRE33 RCL1 NOB1 RRP12 UTP19 6 26 YMR049C (ERB1) 0.00015831 NOP7 NOP2 NOP15 BRX1 4 10 YLR074C (BUD20) 0.000215069 LHP1 ARX1 NSA2 NOP7 NOP15 5 19 YHR066W (SSF1) 0.000693499 MAK5 NOP7 SSF1 DBP9 NOP2 5 24 YKR081C (RPF2) 0.00118628 ARX1 NOP7 NOP15 YTM1 4 16 YBR267W 0.0027734 YBR267W ARX1 2 3 Proteome Localization--Observed Category p-value In Category from Cluster k f nucleus 0.000565755 YBL028C YBL054W YDL063C LYS20 ARX1 YDR365C LCP5 RSC8 NOP7 SYF2 ENP2 SKN7 MPS3 PRY2 SSL1 SPT8 BUD22 NOP2 NOP15 YOL125W RRP6 YOR004W NOB1 DFR1 YTM1 NAN1 HHO1 27 450 Proteome Localization--Predicted+Observed Category p-value In Category from Cluster k f nuc 0.00297292 YBL028C YBL054W CDS1 MAK5 YDL063C CVT20 ARX1 BFR2 YDR365C PDR15 YDR466W LCP5 RSC8 MIG2 YGR058W YGR067C YGR102C NOP7 UTP8 SYF2 ENP2 YIP1 ZUO1 RRP3 SSF1 SKN7 YIL019W MET30 AIR1 YIL091C MPS3 HCA4 PEX2 YKL033W DHR2 YKL098W PRY2 LAS1 SSL1 SPT8 RGR1 DBP9 VID22 RRN11 BUD22 NOP2 NOP15 KRE33 PRP2 YOL125W RRP6 YOR004W RAT1 NOB1 RPO31 YTM1 NAN1 HHO1 APG5 YPL278C RPA135 61 1435 Deletions Consortium (Essentiality, Morphology) Category p-value In Category from Cluster k f essential 1.02103e-06 CDS1 MAK5 CNS1 CTR86 BFR2 YDR365C UTP6 RTT105 NSA2 LCP5 CCA1 RSC8 OLE1 NOP7 UTP8 ENP2 YIP1 ZPR1 RRP3 YIL019W IRR1 MET30 THS1 YIL083C YIL091C MPS3 HCA4 YKL033W DHR2 YKL082C UTP11 LAS1 SSL1 RGR1 UTP13 DBP9 RRN11 ERG13 RRB1 YMR185W NOP2 GCD10 NOP15 KRE33 PRP2 RCL1 BRX1 YOR004W RAT1 NOB1 SGT1 RPO31 RIO1 DFR1 YTM1 RRP12 NAN1 RPA135 MRD1 PIS1 UTP19 61 1101 Morphology - neck abnormalities 0.000943645 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- 2.59548e-06 BFR2 NSA2 NOP7 ENP2 RRP3 SSF1 YIL091C HCA4 UTP11 UTP13 DBP9 NOP2 KRE33 RCL1 RRP6 YTM1 RRP12 MRD1 18 165 Harnicharnpai et al. (2001) - Mol Cell 8:505- 0.00353768 NSA2 NOP7 NOP15 BRX1 YTM1 5 34