Table 1.
Functional classification of genes up-regulated in particular colony phenotypes
| 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 |
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.
*genes are listed in the Additional file 1: Table S1 and discussed in the text.