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Table 1 Functional classification of genes up-regulated in particular colony phenotypes

From: Global changes in gene expression associated with phenotypic switching of wild yeast

  Structured biofilm colony morphotype Smooth colony morphotype
Cell wall SVS1, ASP3-1,-2,-3,-4, BSC1, OSW5 SPS100, CTS1 , FLO9, PFS1, PSA1, ZPS1
Secretory transport & processing BST1, LST7, PER1, CWH41, MNN9, YOL107W, APM4, GVP36, YIP4 BTN2, NCE102, GYP7 , KTR4, PEP12, SNC2, TIM17, TIM21
Metabolism JLP1, MLS1, SNZ1, SNZ2, TPI1 YMR226C, BNA1, ENO1, HPT1, MDH2, RHR2, SOL4 DSF1, PIG2, STR3, CRS5, CUP1-1, FBP26, FOL2, FRE6, HXK1, MTD1, NFS1, SFA1
Amino acids ARG3, ARG4, BAT1, MET17, MET22, ARG1, GDH3, LAP3 GCV1, GCV2, GCV3, SHM2
Lipids & fatty acids INO1 ECI1, POT1, POX1, TES1, VPS66 YNL144C, ERG3, ERG4, HFD1 — AUR1, CEM1, CSG2, SUR1, SUR4
Nucleotides   RNR4 ADE1, ADE2, ADE8, ADE13, PRS3
Transport ITR1, PUT4, VHT1, PDR12, VBA3, ATO2, CAN1, GAP1, MEP2, PIC2 YFL054C HXT15, MUP3, PHO84, THI74, ZRC1, HXT5, HXT17, PHO89, YFL054C, HXT1, HXT2, HXT3, HXT4, HXT6, HXT10, , HXT12, HXT13, MAL11, PHO87, ZRT2
Degradation HSP33, MGR1, NAS2, YSP3 ATG8, BSD2, CIC1, DFG16, GID8, JID1, UMP1, RPN5, RPN13, RPT2, SNA3, VID24, YPT53
Stress response DDR48, GRX3 TSA1, YBL036C, CTA1, SOD2, TSA2 OLA1, HSP42, SPG1, SSA3, SSA4, APJ1, FES1, GPX1, HSP30, HSP78, SSE1, YNL190W, AAD6, CCT5, CPR6, GLO1, GSH1, HSP104 , HSP150, MGE1, OYE3, PST1, RCN2, SED1, STI1, TRX3, YDJ1,YGP1
Regulation   
Translation & RNA processing BRR2, MTQ2, SLF1, DUS4, SPP381, IST3, MRS2, RPP1A, RPR2 PUS2, SLH1, NGL3, RPA135, RSC30, YDR341C, CBF5, SRO9, RPP2A, RPS30B, RPL35B, RRP3, RRP7, SRC1
Signal transduction FAR3 GPA2, MTH1, MRK1, STD1, LST8, RGS2, YMR291W, GLC8, HRK1, KIC1, MTH1, STE7, YAK1
Cell cycle & polarity SHE1 PCL9, HBT1, TAH11, CLG1, CDC13, CDC3, DSE1, VHS1
Transcription CUP9, SFG1, TEC1, YAP7, DAL80, RDS1 YFL052W, HMS1, RLM1, USV1, ZPR1, ALPHA2, CIN5, GIS1, HAP4, OPI1, PHO2, STP2, STP4
- chromatin structure HHF1 TOS8 , IOC4, HHT1, TMA23,TOD6
General transcription   IWR1, RBA50, RPA135, SPT15, SUA7, TAF12, TFA1
Transposons* 8 genes, 10 genes, 1 genes  
Unknown* 7 genes, 5 genes, 17 genes 8 genes, 4 genes, 11 genes
Others   YLR164W, DIA1, DIA3, MRH1, MRPS17, IXR1, PIN3
  1. Genes only expressed differently on the 4th day are in standard letters, genes differently expressed on both the 4th and 7th day are in bold, and genes only expressed differently on the 7th day are italicized.
  2. *genes are listed in the Additional file 1: Table S1 and discussed in the text.