Clustering data with heatmap algorithm for Evidence that COG0325 proteins are involved in PLP homeostasis (Study ST000884)

This analysis uses the 'heatmap.2' function of gplots package in the R statistics environment


The rows are scaled to have mean=0 and standard deviation=1

Factors:

F1Treatment:LB OD 1.0 | SampleType:Cell Pellets | Strain:E.coli Delta glyA (strain VDC6664)
F2Treatment:LB OD 1.0 | SampleType:Cell Pellets | Strain:E.coli Delta glyA (strain​ VDC6665)
F3Treatment:LB OD 1.0 | SampleType:Cell Pellets | Strain:E.coli Delta yggS (strain VDC6594)
F4Treatment:LB OD 1.0 | SampleType:Cell Pellets | Strain:E.coli Delta yggS (strain VDC6595)
F5Treatment:LB OD 1.0 | SampleType:Cell Pellets | Strain:E.coli WT BW25113 (clone1)
F6Treatment:LB OD 1.0 | SampleType:Cell Pellets | Strain:E.coli WT BW25113 (clone 2)
F7Treatment:LB OD 2.0 | SampleType:Cell Pellets | Strain:E.coli Delta glyA (strain VDC6664)
F8Treatment:LB OD 2.0 | SampleType:Cell Pellets | Strain:E.coli Delta glyA (strain​ VDC6665)
F9Treatment:LB OD 2.0 | SampleType:Cell Pellets | Strain:E.coli Delta yggS (strain VDC6594)
F10Treatment:LB OD 2.0 | SampleType:Cell Pellets | Strain:E.coli Delta yggS (strain VDC6595)
F11Treatment:LB OD 2.0 | SampleType:Cell Pellets | Strain:E.coli WT BW25113 (clone1)
F12Treatment:LB OD 2.0 | SampleType:Cell Pellets | Strain:E.coli WT BW25113 (clone 2)
F13Treatment:LB Supernatant (SN) OD 1.0 | SampleType:extracellular supernatant | Strain:E.coli Delta glyA (strain VDC6664)
F14Treatment:LB Supernatant (SN) OD 1.0 | SampleType:extracellular supernatant | Strain:E.coli Delta glyA (strain​ VDC6665)
F15Treatment:LB Supernatant (SN) OD 1.0 | SampleType:extracellular supernatant | Strain:E.coli Delta yggS (strain VDC6594)
F16Treatment:LB Supernatant (SN) OD 1.0 | SampleType:extracellular supernatant | Strain:E.coli Delta yggS (strain VDC6595)
F17Treatment:LB Supernatant (SN) OD 1.0 | SampleType:extracellular supernatant | Strain:E.coli WT BW25113 (clone1)
F18Treatment:LB Supernatant (SN) OD 1.0 | SampleType:extracellular supernatant | Strain:E.coli WT BW25113 (clone 2)
F19Treatment:LB Supernatant (SN) OD 2.0 | SampleType:extracellular supernatant | Strain:E.coli Delta glyA (strain VDC6664)
F20Treatment:LB Supernatant (SN) OD 2.0 | SampleType:extracellular supernatant | Strain:E.coli Delta glyA (strain​ VDC6665)
F21Treatment:LB Supernatant (SN) OD 2.0 | SampleType:extracellular supernatant | Strain:E.coli Delta yggS (strain VDC6595)
F22Treatment:LB Supernatant (SN) OD 2.0 | SampleType:extracellular supernatant | Strain:E.coli WT BW25113 (clone1)
F23Treatment:LB Supernatant (SN) OD 2.0 | SampleType:extracellular supernatant | Strain:E.coli WT BW25113 (clone 2)
F24Treatment:MG OD 0.5 | SampleType:Cell Pellets | Strain:E.coli Delta glyA (strain VDC6664)
F25Treatment:MG OD 0.5 | SampleType:Cell Pellets | Strain:E.coli Delta glyA (strain​ VDC6665)
F26Treatment:MG OD 0.5 | SampleType:Cell Pellets | Strain:E.coli Delta yggS (strain VDC6594)
F27Treatment:MG OD 0.5 | SampleType:Cell Pellets | Strain:E.coli Delta yggS (strain VDC6595)
F28Treatment:MG OD 0.5 | SampleType:Cell Pellets | Strain:E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)
F29Treatment:MG OD 0.5 | SampleType:Cell Pellets | Strain:E.coli WT BW25113 (clone1)
F30Treatment:MG OD 0.5 | SampleType:Cell Pellets | Strain:E.coli WT BW25113 (clone 2)
F31Treatment:MG OD 1.0 | SampleType:Cell Pellets | Strain:E.coli Delta glyA (strain VDC6664)
F32Treatment:MG OD 1.0 | SampleType:Cell Pellets | Strain:E.coli Delta glyA (strain​ VDC6665)
F33Treatment:MG OD 1.0 | SampleType:Cell Pellets | Strain:E.coli Delta yggS (strain VDC6594)
F34Treatment:MG OD 1.0 | SampleType:Cell Pellets | Strain:E.coli Delta yggS (strain VDC6595)
F35Treatment:MG OD 1.0 | SampleType:Cell Pellets | Strain:E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)
F36Treatment:MG OD 1.0 | SampleType:Cell Pellets | Strain:E.coli WT BW25113 (clone1)
F37Treatment:MG OD 1.0 | SampleType:Cell Pellets | Strain:E.coli WT BW25113 (clone 2)
F38Treatment:MG Supernatant (SN) OD 0.5 | SampleType:extracellular supernatant | Strain:E.coli Delta glyA (strain​ VDC6665)
F39Treatment:MG Supernatant (SN) OD 0.5 | SampleType:extracellular supernatant | Strain:E.coli Delta yggS (strain VDC6594)
F40Treatment:MG Supernatant (SN) OD 0.5 | SampleType:extracellular supernatant | Strain:E.coli Delta yggS (strain VDC6595)
F41Treatment:MG Supernatant (SN) OD 0.5 | SampleType:extracellular supernatant | Strain:E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)
F42Treatment:MG Supernatant (SN) OD 0.5 | SampleType:extracellular supernatant | Strain:E.coli WT BW25113 (clone1)
F43Treatment:MG Supernatant (SN) OD 0.5 | SampleType:extracellular supernatant | Strain:E.coli WT BW25113 (clone 2)
F44Treatment:MG Supernatant (SN) OD 1.0 | SampleType:extracellular supernatant | Strain:E.coli Delta glyA (strain VDC6664)
F45Treatment:MG Supernatant (SN) OD 1.0 | SampleType:extracellular supernatant | Strain:E.coli Delta glyA (strain​ VDC6665)
F46Treatment:MG Supernatant (SN) OD 1.0 | SampleType:extracellular supernatant | Strain:E.coli Delta yggS (strain VDC6594)
F47Treatment:MG Supernatant (SN) OD 1.0 | SampleType:extracellular supernatant | Strain:E.coli Delta yggS (strain VDC6595)
F48Treatment:MG Supernatant (SN) OD 1.0 | SampleType:extracellular supernatant | Strain:E.coli double mutant Delta yggS Delta glyA VDC strain​ (strain VDC6658)
F49Treatment:MG Supernatant (SN) OD 1.0 | SampleType:extracellular supernatant | Strain:E.coli WT BW25113 (clone1)
Data matrix
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