TABLE 3.

Functional distribution of PFA-responding genes

GO categoryaPFA data set frequency (%)Genome frequency (%)P valueCaCl2-, AMD-, and calcineurin/Crz1-associated genes
Upregulated genes
    Response to stress23.6312.932.34 × 10−7AGX1b,c ALD3b,c ARK1c,d ATG5b,c,d BAG7b,c,d DDR2b,c DDR48b DOT5b ECM4b FMP45b,c FMP46b GRE1b GRE2b,c GTT1b HBT1b HOR2b,d HSP12b,c HSP26b,d HSP31b,c LAP4b PBI2b PRB1b,c,d PRX1b RSB1c RTA1b,c,d SCS3d SDS24b,c SNZ1b,d SPI1b,c,d TOS3b UBC5b UBI4b UGA2b XBP1c,d YBR016Wd YBR056Wd YDL010Wd YER185Wb,c,d YET2b,c,d YGP1b,d YHR138Cb,c,d YJL068Cb,d YJL144Wb,c,d YJR096Wb YJR107Wd YMR090Wb YOR052Cb,c,d YOR338Wb,d
    Transport20.2119.115.19 × 10−2ADY2c ARK1c,d ATG5b,c,d ECM27c,d ENA5c,d FLC1d GIT1d GSP2b GYP7b,c,d HES1d HXT5b,c,d IMP2d JEN1c KHA1b,d MEP1b,c,d MIG2c ODC1b PBI2b PDR10c,d PEP12b,c,d PMC1b,d PRM8b,c,d RCR1b,c,d RSB1c SDS24b,c SGE1b,d UBC5b VPS36c,d YBR287Wb,c,d YDL010Wd YER185Wb,c,d YET2b,c,d YMR034Cc YOL162Wb,d YPT53b,c,d
    Carbohydrate metabolism10.275.77.35 × 10−4AMS1b,c,d CAT8c,d CHS1b,c,d CRH1d GND2b GSC2d HOR2b,d MAL33c MIG2c MNT4b,c,d NRG1b,c OCH1d SGA1b SHC1b TOS3b YBR056Wb,d YGR043Cb,c YJR096Wb YMR085Wc,d
    Transcription8.5611.671.87 × 10−2CAT8c,d CRZ1d CSE2b,d CSR2c,d CUP2b,c,d DOT5b MAL33c MIG1c NRG1b,c PCL5b,d REG2c VPS36c,d XBP1c,d YER184Cb,c,d
    Protein modification8.2211.052.32 × 10−2ARK1c,d ATG5b,c,d CMK2b,c,d HAL5c,d MNT4b,c,d OCH1d STB2d TOS3b UBC5b UBI4b UBP5d VHS1c YGR052Wb,c YMR291Wc
    Organelle organization7.5318.091.26 × 10−7ARK1c,d BNA2b,d CSE2b,d GSP2b PBI2b PEP12b,c,d STB2d THI4b,d YHR138Cb,c,d
    Amino acid metabolism6.854.21.07 × 10−2AGX1b,c ALD3b,c ARO10b,d ARO9b PUT1b,c,d SNO1d SPS100b,c,d UGA2b YGP1b,d YHR033Wb YMR085Wc,d YMR090Wb
    Membrane organization5.824.013.31 × 10−2ARK1c,d ATG5b,c,d HES1d PBI2b PEP12b,c,d RSB1c SDS24b,c UBC5b YHR138Cb,c,d YPT53b,c,d
    Cell wall organization5.483.271.55 × 10−2CHS1b,c,d CRH1d CSR2c,d ECM27c,d ECM4b FMP45b,c GSC2d OSW2b,c,d RCR1b,c,d SHC1b SPS100b,c,d YLR194Cb,c,d YPS3b,c,d
    Sporulation5.142.636.29 × 10−3FMP45b,c GSC2d OSW2b,c,d PRB1b,c,d SGA1b SHC1b SPS100b,c,d UBC5b UBI4b UBX6b YNL194Cc YOR388Wb,d
Downregulated genes
    Cell cycle15.099.819.85 × 10−3ARP1c CLB1b,c CLB2b,c CLB6b,c DAD2c FAR1b,c FUS3b,c,d HOF1b,c KAR4c MAK16b,c MCD1b,c NDJ1b,c NIS1b,c PCL9b,c POL30b,c PTC2b,c SPC24b,c SPO16c SUN4b,c TUB1b,c YGR271C-Ac YHP1b,c
    Ribosome biogenesis15.0911.984.45 × 10−2ADE4b,c ALB1b,c ARP1c CYB5b,c DFR1b,c EBS1b,c FAF1b FAR1b,c FRE1b,d FYV7b,c GFD2b,c MAK16b,c MRT4b,c MTD1b,c PHO3b,c RPS28Bb,c SER2b,c SRD1b,c YGR271C-Ac YOR305Wc YPL279Cb,c ZRT2b
    Conjugation11.952.05.58 × 10−10AGA1b,c AGA2b,c FAR1b,c FIG1b,c FIG2b FUS1c FUS3b,c,d KAR4c MF(ALPHA)2b,c MFA1b,c PRM1c PRM2b PRM3b PRM6b,c SAG1b,c SST2b,c STE2b,c STE3c TUB1b,c
    Translation11.3217.381.03 × 10−2AAC3b,c ADE17c ADH4c ADK2c ANB1b,c EBS1b,c FAR1b,c FSH1b,c HEM13b,c PMU1c PTC2b,c RPS28Bb,c SHM2b,c SST2b,c YMR010Wc YOR302Wb
    Amino acid metabolism8.184.29.70 × 10−3ACO1b,c ADE4b,c ADH4c DFR1b,c DIC1c GCV1c GCV2c MHT1b SER2b,c SHM2b,c
    Signal transduction7.554.83.86 × 10−2FAR1b,c FUS3b,c,d MF(ALPHA)2b,c MFA1b,c MSB4b,c PTC2b,c RPI1b,c SST2b,c STE2b,c STE3c TEC1b,c YIL169Cb
    Meiosis5.663.012.94 × 10−2CLB1b,c KAR4c NDJ1b,c POL30b,c SPO16c TUB1b,c YHP1b,c
  • a Data (for 296 upregulated genes and 161 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 value, ≤0.05) with a PFA data set frequency of ≥5% are listed.

  • b Gene responsive to 200 mM CaCl2 (15 and 30 min) (37).

  • c Gene responsive to 15 μM amiodarone (10 min) (38).

  • d Gene associated with calcineurin (37) and/or Crz1 (http://www.yeastract.com) (34).