Table 5.
Overrepresented (p-value < 0.01) biological categories based on the MIPS and GO databases of the Functional Specification Instrument for 5G and 15G exposures of select significantly resistant and sensitive strains, as well as any observed overlap strains between 5G and 15G (Ashburner et al., 2000; Mewes et al., 2002; Robinson et al., 2002).
| Category | p-value | Name of genes in category | Number of genes observed in category | Number of genes in category |
|---|---|---|---|---|
| 5G SENSITIVE | ||||
| GO Molecular Function | ||||
| Transferase activity [GO:0016740] | 0.000779 | KIN3 FMT1 ALG3 CST26 EHT1 DPB3 KCC4 FEN1 BUD23 MGT1 KIN1 MTQ2 AKR1 TRP4 DOT1 EMI2 HIS1 TMT1 RIM15 CMK1 YFR018C TAN1 NAT2 CHO2 STE20 ARD1 YCK1 PFK26 HPM1 POT1 DAL7 AIM22 IKS1 TPK1 SET2 YJL218W ELM1 AAT1 TPK3 KTR2 AYT1 SHM2 RCK2 NNT1 TAL1 SUR4 ERG6 TRM9 APT1 URA5 TDA1 CPT1 ARE2 PFA4 GAS5 PKH2 PAP2 OST3 ABP140 TUM1 MEK1 SKS1 BTS1 ISR1 TAZ1 GPH1 | 66 | 611 |
| NADPH dehydrogenase activity [GO:0003959] | 0.005429 | OYE2 OYE3 | 2 | 2 |
| GO Biological Process | ||||
| Chromatin silencing at telomere [GO:0006348] | 0.002979 | SWD1 DPB3 DOT1 DOT6 RAD6 ASF1 SPT10 IES3 MEC3 YAF9 SAS5 | 11 | 58 |
| MIPS Functional Classification | ||||
| Meiotic recombination [10.01.05.03.01] | 0.005619 | MSH4 DST1 SAE2 RIM4 SAE3 REC104 RAD52 RAD50 | 8 | 38 |
| Organization of chromosome structure [42.10.03] | 0.0058 | SWD1 RIF1 SGF29 SPT3 DOT1 IES1 EST3 SET2 NAP1 IES3 SPT8 RAD52 YKU70 RAD50 | 14 | 90 |
| Cytoplasm [725] | 0.001171 | ATS1 DRS2 CLN3 FLC2 APN2 PIN4 ALG3 SRO77 UGA2 GAL10 SCO2 RPS11B UBP14 TAT1 SLM4 RPL19A OPY1 YBR138C ARA1 ARL1 PEX32 EHT1 YBR225W UBX7 DPB3 DCC1 FRM2 FEN1 BUD23 RPN4 YDL063C PEX19 BDF2 RPL13A CYK3 RDI1 PPH22 RTN2 YDL211C GDH2 DTD1 FMP45 PTP1 YDL241W GRX3 KIN1 MTQ2 RSM24 COQ4 BTT1 AKR1 HNT2 ASP1 YDR336W YDR338C YPS7 TRP4 EFT2 SAC7 URH1 SIZ1 CYM1 DOT1 SSN2 YDR444W RPS18A EMI2 IRC4 GIM4 GLY1 YEL047C TCA17 DOT6 SWI4 SLX8 YER137C RTR1 YER156C YER163C TMT1 DEG1 VTC2 BLM10 WWM1 YFL012W HSP12 LPD1 GAT1 BUD27 RIM15 RPL22B FET5 EMP47 CMK1 YFR016C LSB3 DUG1 RAD6 RPL9A SAE2 TAN1 SCM4 YGR117C NAT2 RPL24B CHO2 YHB1 GND2 RAD2 SLH1 STE20 RIM4 SNF6 ARD1 YHI9 AAP1 YCK1 OYE2 GND1 RPN10 YIL089W PFK26 HPM1 HOS4 POT1 MET28 DAL81 YVH1 HYR1 MAD3 YJL043W TDH1 YJL055W IKS1 RPE1 SPT10 RPS21B TPK1 REE1 YJL218W CPR7 YMR1 YJR111C YJR154W YKL070W KTI12 PMU1 RPS27A TPK3 SAC1 YKR041W NAP1 MSA2 YKR078W MLP1 YKR096W TPO1 MLH2 YLR036C SHM2 CCW12 ACE2 TFS1 HCR1 CCC1 MAP1 RCK2 NNT1 RPS30A TMA10 VRP1 NIT3 TAL1 ATG33 DIF1 RPL6B YLR456W ERG6 TRM9 APT1 YOX1 YML079W URA5 YMR074C PGM2 YMR114C ATG16 YMR244C-A GFD1 YKU70 TDA1 YMR295C DYN3 ELP6 PUB1 SLM2 MLF3 OCA1 YAF9 YNL108C YNL122C JJJ1 RAD50 PDR17 CAF120 HCH1 PUS4 KRE1 SIN3 PKH2 RPS19A WHI2 VHS3 DCS2 SAS5 RPL33B ABP140 TUM1 HNT3 CAF20 RPL20B VTS1 LSP1 CHL1 TAE2 HST2 SKS1 SVL3 SRL4 ARL3 BTS1 RPL21B SSE1 GDE1 BEM4 OYE3 FLC1 NEW1 KEL3 ANT1 NCE102 GPH1 MET16 YPR174C AQY1 | 245 | 2879 |
| 15G SENSITIVE | ||||
| GO Molecular function | ||||
| Glycine hydroxymethyltransferase activity [GO:0004372] | 0.001125 | SHM1 SHM2 | 2 | 2 |
| Pyridoxal phosphate binding [GO:0030170] | 0.002904 | SHM1 ALT2 GLY1 IRC7 SHM2 BNA5 | 6 | 43 |
| Zinc ion binding [GO:0008270] | 0.004272 | HIS4 ADH7 NRP1 NRG1 SAN1 AST2 GAT1 DMA1 AIR1 ASG1 GAT4 DAL81 ACE2 ECM22 CAT8 FAP1 GIS2 PFA4 YRM1 ULS1 | 20 | 314 |
| Sequence-specific DNA binding transcription factor activity [GO:0003700] | 0.00656 | GAT1 HAC1 XBP1 ASG1 GAT4 DAL81 PHD1 ECM22 CAT8 FAP1 YRM1 | 11 | 138 |
| Metal ion binding [GO:0046872] | 0.009408 | HIS4 ADH7 NRP1 NRG1 SAN1 GAT1 DMA1 HOP1 AIR1 ASG1 GAT4 DAL81 ELM1 ELF1 JLP1 IZH3 PDC1 EMP46 ACE2 ECM22 IRC21 CAT8 FAP1 NRK1 GIS2 FRE4 PFA4 DNL4 TCB1 YRM1 ULS1 FMP30 PDH1 | 33 | 647 |
| Sequence-specific DNA binding [GO:0043565] | 0.009413 | NRG1 GAT1 HAC1 XBP1 ASG1 GAT4 PHD1 BAS1 ACE2 ECM22 CAT8 YRM1 | 12 | 165 |
| Catalytic activity [GO:0003824] | 0.009792 | SHM1 HIS4 ADH7 PHO13 TRP1 ARO3 TPS2 ALT2 GLY1 AST2 IRC7 SGA1 IRC24 LAS21 YKL071W YKL107W SIS2 PDC1 SHM2 BNA5 EXG1 CDA1 GRE2 LSC1 GDB1 | 25 | 455 |
| GO Biological Process | ||||
| l-serine metabolic process [GO:0006563] | 0.001125 | SHM1 SHM2 | 2 | 2 |
| Protein ubiquitination involved in ubiquitin-dependent protein catabolic process [GO:0042787] | 0.003238 | SAN1 RMD5 UBC8 ELC1 | 4 | 19 |
| Cell redox homeostasis [GO:0045454] | 0.003414 | PRX1 TRX2 POR2 AHP1 GLR1 | 5 | 31 |
| Drug transmembrane transport [GO:0006855] | 0.005065 | YDR338C QDR2 YRM1 | 3 | 11 |
| Glycine metabolic process [GO:0006544] | 0.006456 | SHM1 SHM2 | 2 | 4 |
| GO Cellular Component | ||||
| Membrane [GO:0016020] | 0.003977 | UIP3 SCS22 FIG2 MSS2 RGT2 RTN2 UGA4 ENT5 SPR28 OMS1 YDR338C ATP17 QCR7 YEA4 PIC2 YFR012W QCR6 KEX1 YPT32 TRX2 PHB2 APL6 PUT2 HXT1 CBR1 FIS1 KTR7 YIL089W SLM1 POR2 QDR2 ATG32 DAL4 LAS21 NUP100 YKL107W PXA2 CAF4 GAP1 TGL4 SPO75 YEH2 IZH3 PET309 EMP46 EMP70 ENT2 ECM22 YLR283W NUP2 SMA2 PLB1 YET2 ATP25 AIM36 INP2 YMR166C MFA2 LEM3 ATO2 FRE4 PFA4 TIR4 VPS5 TCB1 KTR1 FMP30 COX11 ATG5 UIP4 FLC1 SAM3 JID1 YPR174C | 74 | 1671 |
| MIPS Functional Classification | ||||
| C-1 compound anabolism [01.05.05.04] | 0.003301 | SHM1 SHM2 | 2 | 3 |
| Detoxification by export [32.07.05] | 0.003301 | QDR2 YRM1 | 2 | 3 |
| Oxygen and radical detoxification [32.07.07] | 0.006587 | PRX1 TRX2 AHP1 | 3 | 12 |
| MIPS Subcellular Localization | ||||
| Cytoplasm [725] | 0.002267 | UIP3 PRX1 SEA4 NGR1 FRM2 HIS4 SRO9 YCL042W ADH7 BUG1 MSS2 UBP1 LDB17 NRP1 YDL177C RTN2 DTD1 PHO13 TRP1 ARO3 NRG1 TPS2 BMH2 ALT2 GIR2 ENT5 CSN9 RMD5 YDR336W YDR338C SSN2 RMT2 UBC8 YEL043W GLY1 SAP1 AST2 ECM32 GAT1 HAC1 FAR7 QCR6 KEX1 YPT32 NMA2 ASN2 YGR153W TRX2 APL6 EFM1 ARD1 DMA1 LSM12 TDA11 AIR1 YIL089W XBP1 SLM1 RPI1 DJP1 DAL81 IRC24 RPS4A YKL063C YKL071W YKL091C YKL107W TPK3 NAP1 TRM2 SIS2 TGL4 YLR031W PDC1 SHM2 AHP1 ACE2 RNH203 YKE2 CPR6 ECM22 BNA5 RPN13 DAK1 YML079W PLB1 IRC21 RPL15B YMR124W YMR147W ATG16 YMR166C ZDS1 CAT8 PUB1 NRK1 NPR1 GIS2 LEM3 SSK2 PKH2 GRE2 SHE4 CKA2 VPS5 EFT1 YRM1 GSP2 PAC1 TAE2 ELC1 GLR1 RTT10 UIP4 FLC1 PDH1 YPR174C GDB1 | 118 | 2879 |
| MIPS Protein Complexes | ||||
| Complex Number 160 [550.2.160] | 0.000146 | AHP1 MEC3 DNL4 | 3 | 4 |
| 15G AND 5G SENSITIVE OVERLAP | ||||
| GO Molecular Function | ||||
| d-tyrosyl-tRNA(Tyr) deacylase activity [GO:0051500] | 0.004998 | DTD1 | 1 | 1 |
| Glycine hydroxymethyltransferase activity [GO:0004372] | 0.009971 | SHM2 | 1 | 2 |
| GO Biological Process | ||||
| d-amino acid catabolic process [GO:0019478] | 0.004998 | DTD1 | 1 | 1 |
| l-serine metabolic process [GO:0006563] | 0.009971 | SHM2 | 1 | 2 |
| MIPS Protein Complexes | ||||
| Complex Number 2, probably cell cycle [550.1.2] | 0.009971 | DTD1 | 1 | 2 |
All strains included in this analysis were sensitive in at least one of the six treatments. Bolded genes correspond to those whose response to BaP was confirmed by individual exposure of the corresponding deletion strain.