The synthetic genetic interaction spectrum of essential genes

Armaity P. Davierwala, Jennifer Haynes, Zhijian Li, Renee Brost, Mark D. Robinson, Lisa Yu, Sanie Mnaimneh, Nicolle Preston, Hongwei Zhu, Yiqun Chen, Xin Cheng, Grant Brown, Charles Boone, Brenda J. Andrews and Timothy R. Hughes


Abstract
The nature of synthetic genetic interactions involving essential genes - those required for viability - has not been previously examined in a broad and unbiased manner. We crossed yeast strains harboring promoter-replacement alleles for more than half of all essential yeast genes to a panel of 30 different mutants with defects in diverse cellular processes. The resulting genetic network is biased towards interactions between functionally-related genes, enabling identification of a previously-uncharacterized essential gene (PGA1) required for specific functions of the endoplasmic reticulum. However, there are many interactions between genes with dissimilar functions, suggesting that individual essential genes are required for buffering of many cellular processes. The most striking feature of the essential synthetic genetic network is that it has an interaction density five times that of non-essential synthetic genetic networks, indicating that the majority of yeast genetic interactions involve at least one essential gene.

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Binary Matrix of Genetic Interactions
List of Genetic Interactions
Tet vs. ts Summary
Tet ts Array list
Query Strains (Supplementary Table 1)
Tet Strains
Methods
README
ZIP file containing all above files

Images
ACT1 ALG7 ASK1 COG4 ERG1 FRS1 HRT1 LSM4 NOP14 ORC6 PNO1 RAD3 RFT1 RNA14 RRP42 SAS10 SLD5 SLY1 SSU72 SWP1 YGR198W YHR122W YJL097W
ARL3 BET5 COG2 OST2 TRS20
ARP2 ABD1 APC11 AVO1 CDC15 CDC5 CWC22 HRT1 HSC82 HSP60 LAS17 MAK5 MET30 NOP14 PFY1 PLP2 PRP42 PRP9 RLP7 RPR2 SRP21 SUA7 TEM1 YEF3 YGR198W
BIM1 BRR2 CKS1 POL12 POL30 RER2 SSU72 STU1
BNI1 BRX1 CDC19 CFD1 COG4 COP1 DPM1 DRS1 ERG1 GRC3 LCB2 LPD1 MAK16 NAN1 NOP7 PFY1 PLP2 POP1 PRE5 RER2 RFT1 SDA1 SEC10 SEC11 SEC15 SEN34 SRP72 SSU72 THS1 UTP15 UTP20 UTP22 UTP4 UTP9 YNL158W
CDC12 APC11 CDC15 CDC9 CDC91 DOP1 ESS1 FMP28 GPI16 HRT1 LAS17 LCB2 MEC1 MES1 MOT1 NOC3 NUP192 NUP85 ORC6 PAM18 PAN1 PFY1 PRO3 PRP11 PRP9 PSF2 PWP1 PXR1 REB1 RER2 RIM2 RPS31 SEC2 SEC3 SSU72 TAF1 TAF2 TEN1 UGP1 UTP4 UTP6 UTP9 YBR070C YDR267C YGL245W YML125C YOL022C ZPR1
CDC40 CKS1 FRQ1 GPI10 GWT1 HSP60 KAP95 PRP16 PRP24 PRP38 PSF2 RFA2 RTS2 TSC11 YGL047W (Data from Mnaimneh et al., Cell 2004) Images in PPT file
CDC42 APC11 DBP10 FAD1 HRT1 HSC82 RPC40 RPM2 SEC3 SIT4
CSM3 DPB11 POP1 RFA2 RPT2
DBP10 CDC53 POL5
ERG11 CDC27 CDC37 CDC91 DOP1 DPS1 DRS1 ECM16 ERG7 GLE1 GPI16 GPI2 IPI1 LSM4 MOB1 MVD1 NCP1 NOC3 NOP2 NOP8 NUG1 PFY1 PLP2 POL30 POP1 POP4 PWP1 PXR1 RER2 RNA1 RPC11 RPC17 RPC31 RPC53 RRP14 SEC2 SMD3 SRB6 SRP21 TAF7 TOM22 TRM5 UTP11 YML125C YNL158W YNL247W ZPR1
EXO84 BET3 CKS1 MET30 PFY1 POL30 SEC1 SWP1 YJR141W
KRE1 RER2 SEC2 SEC5 UGP1 YNG2
LOS1 POP5 TAF3
LRP1 CCA1 CDS1 CWC22 DRS1 LCP5 NOC2 NOP7 POL30 POL5 PRO3 PRP46 PWP1 RNA14 RRS1 RSC9 SEC18 SMD2 SMD3 TEL2 TFG2 TRM5 URB2 UTP11 UTP4 YNG2 YNR054C YOR004W
MRC1 CDC54 DPB11 MYO1 POL30 SLD5
NIP7 ABD1 APC11 BET3 CCA1 CDC16 CFT2 CKS1 CWC22 ENO2 ERG27 EXO84 GOD1 MCD4 MVD1 PDS5 POL12 POL30 POL5 PRO3 PRP16 PRP24 RAD3 RIM2 RIX7 RNA14 RNA15 RPL17A RSC9 SLD2 SRB6 TFB1 TIM50 YIP1
NOP1 APC11 BET3 CWC22 DBF4 DHR2 ERG25 GPI11 JIP5 LCP5 MAS1 MET30 MSS4 NOP8 NPL4 PRP16 PRP28 PRP38 RAD3 RFA2 RFC3 RKI1 RPL17A SAS10 SEC17 SEC5 SRB7 TAF1 UGP1 UTP11 YNR054C YOR004W YOR287C
PRT1 CDC5 NET1 PRO3 SRB6 SUI2 YNL158W
RAD50 CDC45 CDC9 POB3 RFC2
RFC5 ALG2 CDC27 CDC45 CDC9 DPB11 DPS1 DUT1 IST2 MOT1 MYO2 NOP14 NSE1 NUP192 ORC3 POL1 POL30 RFA2 RFC2 RHC18 RIX1 SCH9 SLD5 SPC98 YHR122W
RPA49 CDC45 CWC25 DED81 DPB11 ENO2 IPI1 MET30 NUF2 OST2 POL30 RNT1 RRN11 RRN3 RSC9 SEC5 SPC19 SPC98 SPT16 UBC1 YDR412W YNL247W
RPS17A APC11 BRR2 CLF1 CWC22 DOP1 POL30 PRO3 PRP11 PRP38 PRP42 PRP5 RIM2 RTS2 SNU56 SPC98 TAF7 UGP1 YBR070C YML6
SEC1 BET3 CDC45 DBF4 GPI2 MEC1 MET30 MYO2 NOP14 PFY1 SEC2 SEC5 SEC8 SWP1 TAF10 TRM5 YDR267C YGR198W YNG2 ZPR1
SEC15 ARP7 BET3 CDC5 CDS1 CKS1 ECM16 EFB1 ERD2 ERG7 EXO84 GLE1 GPI2 HRT1 IPI1 MET30 MPE1 MYO2 MRT4 NOC2 NOP15 PDS5 PFY1 POB3 POL30 PRP16 RPC11 RPC40 RPC53 RPF1 RPR2 RSC9 SEC2 SEC5 SEC8 SEN54 SRB6 SSU72 SWP1 TAF10 TAH18 TFB1 TOR2 UTP4 UTP9 YBR070C YDR196C YGL047W YGR198W YJR141W YNG2 YNL158W YNL313C ZPR1
SEC18 BET5 CDC91 CKS1 DOP1 ERG7 GPI2 HRT1 MRT4 PFY1 RPC40 RPF1 RSC9 SAS10 SSU72 TFG2 YGR198W
SEC7 BET5 CDC45 CDC91 DBF4 DHR2 DOP1 DRS1 EFB1 ERG1 ERG7 GPI2 LAS17 MEC1 MTR3 MYO2 NOC2 NOG2 NOP15 NUG1 PFY1 POB3 POL30 PWP1 RFT1 RIA1 RPF1 RPL18A RSC9 SEC12 SEC3 SLD2 SPC34 SSU72 SUI2 THS1 TRM5 TUB1 UTP15 UTP5 UTP9 YNL158W
SET2 BET3 CEG1 COG2 MET30 MPS1 PRP38 RSC9 SED5 SLU7 SPC98 TAF7 TFB1 TFG1
SLT2 ALG7 CDC91 ERG27 ERG7 ERO1 GPI1 GPI11 GPI16 MCD4 MOT1 NCP1 PFY1 PRP16 RER2 ROT1 RPC10 SEC15 SEC2 SEC5 SEC8 SWP1 TAF10
SRB6 DUT1 POB3 POL30 TAF13

TET vs. TS Images
ARP2 CDC11-tet CDC25-tet CDC34-tet CDC42-tet RFC5-tet SEC14-tet ABD1-tet CDC5-tet ABD1-5-ts CDC11-2-ts CDC5-1-ts CDC25-1-ts CDC34-1-ts CDC42-1-ts RFC5-1-ts SEC14-3-ts
BNI1 CDC11-tet CDC42-tet RNA1-tet CDC19-tet SEC10-tet SEC15-tet CDC19-1-ts CDC3-1-ts SEC10-2-ts SEC15-1-ts CDC11-2-ts CDC11-3-ts CDC11-5-ts CDC42-1-ts RNA1-1-ts
RFC5 ABD1-tet CDC16-tet CDC27-tet CDC2-tet CDC34-tet CDC6-tet DBF4-tet DFR1-tet KIN28-tet MCM10-tet CDC9-tet CDC34-1-ts CDC9-1-ts CDC27-1-ts CDC27-2-ts KIN28-ts ABD1-5-ts CDC16-1-ts CDC2-7-ts CDC6-1-ts DBF4-1-ts DFR1-td-ts MCM10-1-ts
SEC1 DBF4-tet SEC15-tet SEC2-tet SEC3-tet SEC8-tet DBF4-td-ts SEC15-1-ts SEC2-41-ts SEC3-2-ts SEC8-9-ts
SEC15 CDC42-tet SEC1-tet SEC3-tet SEC10-tet SEC5-tet SEC2-tet SEC8-tet CDC5-tet EXO84-tet SEC1-1-ts CDC42-1-ts CDC5-1-ts EXO84-2-ts SEC3-2-ts SEC8-9-ts SEC5-24-ts SEC10-2-ts SEC2-41-ts