Table 1.
Functional distribution of 6-NDA-responding genes in S. cerevisiae
| GO terma | 6-NDA data set frequency (%) | Genome frequency (%) | P value | Genes annotated to the GO termb |
|---|---|---|---|---|
| Upregulated genes | ||||
| Response to stress | 17.29 | 11.04 | 4.53E−06 | ATG1, ATG20, ATG29, ATG5, ATG8, CTT1, DAK1, DDR2, DDR48, GAD1, GPX1, GRE1, GRE3, GRX1, HIM1, HOR2, HSP104, HSP12, HSP26, HSP42, HSP78, HSP82, IMP2', MAG1, ORM2, POL4, PRX1, PTP2, RAD28, REV3, RPH1, RPN4, RTA1, SRX1, SSA1, SSA4, SSE2, STE11, TDP1, TPS1, TPS2, TRX3, TSA2, UBC5, UBI4, XBP1, ZTA1 |
| Carbohydrate metabolism | 7.71 | 5.40 | 5.52E−03 | AMS1, ARA1, ATH1, CAX4, DAK1, ERR3, GCY1, GDE1, GND2, GRE3, GSC2, HOR2, KTR2, MNT4, NTH1, OCH1, PCK1, PFK26, PYK2, RBK1, RMD5, SGA1, SOR2, TKL2, TPS1, TPS2, UBC8, VID28, VID30, YPI1 |
| Cell wall organization | 7.33 | 4.01 | 1.38E−04 | ADY3, CDA1, CHS1, CRH1, CRR1, CWP1, DFG5, DIT1, DIT2, ECM27, ECM4, ECM8, FLC1, FLC2, FMP45, GAS4, GIP1, GSC2, HPF1, HRD1, MPC54, OSW2, PIR3, PST1, RCR1, SED1, SPR28, SPR3, SPS100, SPS22, SVS1, YPK2, YPS3 |
| Lipid metabolism | 5.45 | 3.93 | 1.76E−02 | ATF1, CAT2, FAA2, FOX2, GDE1, INO1, INO2, IPT1, ISC1, IZH2, IZH4, MGA2, OPI10, PLB1, PLB3, POT1, ROG1, SCS3, SPO1, SPS19, SUR1, TES1, TGL2, YDC1, YSR3 |
| Downregulated genes | ||||
| Transport | 26.74 | 20.97 | 4.12E−03 | AGP1, AQR1, ATO3, ATR1, AUS1, CAN1, DAL5, DIP5, DUR3, FCY2, FET3, FTR1, FUI1, GAP1, GNP1, HXT4, LYP1, MCH4, MEP1, MEP2, MEP3, MMP1, MUP1, MUP3, OPT1, OPT2, PDR12, QDR2, SAM3, SEO1, SSU1, SUL2, VHT1, ZRC1, ZRT1, ZRT2 |
| Translation | 19.78 | 16.39 | 2.04E−02 | AGP1, ARG3, CPA2, HOM3, MAK16, MET13, MET14, MET2, MET3, MET32, MUP1, RLI1, RPL18B, RPL22B, RPM2, SAM3, SER33 |
| Amino acid metabolism | 15.75 | 4.99 | 2.3E−11 | AAT1, ACO1, ACO2, ARG3, ARG5,6, ARG8, ASN1, CPA2, DUR1,2, ECM17, GAP1, GCV2, GDH1, GLT1, HIS6, HOM3, LEU9, MET1, MET10, MET13, MET14, MET16, MET2, MET22, MET28, MET3, MET32, MET8, MHT1, SER33, SSU1 |
| Cell cycle | 12.82 | 10.40 | 3.22E−02 | AMN1, BUD9, CDC47, CLB1, CLB6, CSM2, DAD3, DSE1, DSE3, EGT2, FAR1, FKH1, HOF1, KAR4, KAR9, KCC4, MCM3, MCM6, NIS1, NNF1, PAP2, PDS1, RMD6, SDA1, SGO1, SPO16, SPS4, SUN4, TRF5, UME6 |
| Conjugation | 5.86 | 1.93 | 7.2E−05 | AGA1, AGA2, DSE1, FAR1, FIG1, FIG2, FUS1, FUS3, KAR4, MF(ALPHA)2, MFA1, PRM1, PRM2, SAG1, SST2, STE2 |
a
Data (538 upregulated genes and 277 downregulated genes) were organized into GO-based biological process categories using the GO Term Mapper tool (http://go.princeton.edu/cgi-bin/GOTermMapper). Significantly overrepresented categories (P ≤ 0.05) with a 6-NDA data set frequency of ≥5% are listed.
b
Within each GO category, a subset of genes are shown that are relevant to the overall biological response to 6-NDA.