CSB.DB: Matrix

Matrices@CSB.DB: E.coli Matrix Information Page

This page provides background information about the Escherichia coli gene expression data matrices which are the basis for the co-response analyses. For further information about particular experiments follow the given link.

E.coli Matrices

To get information of your choice for the Escherichia coli gene expression data matrices use the links listed below.

Matrix smd4501 (m4501): processing | experiments |

Matrix smd4502 (m4502): processing | experiments |

Matrix asap96a (m96a): processing | experiments |

Matrix asap96b (m96b): processing | experiments |

Matrix asap96b: Processing

Escherichia coli - Expression Data Matrix asap96b (m96b): Processing

Transcript profiles of Matrix asap96b (m96b) were derived from the ASAP database (Glasner et al., 2003) and originated from colour-coded cDNA hybridisation technology. The transcript profiling experiments of asap96b (m96b) covered miscellaneous stress treatments, application of antibiotics, comparison of media and growth conditions, as well as characterisation of mutants (Allen et al., 2003). Profiles were normalized and log base 2 transformed. Matrix asap96b (m96b) comprised 50 experiments, which were described by 4290 genes (Steinhauser et al., 2004a). Normalised transcript intensities were log base 2 transformed. Co-Response analyses were performed on range normalised (genes) matrix.
For detailed description of the experiments please query the ASAP database.

Matrix asap96b: Experiments

Escherichia coli - Expression Data Matrix asap96b (m96b): Experiment List

For detailed description of the experiments please query the ASAP database.

CSB.DB ID	Group	Experiment Description
100	1	15 degree cold shock 10 minutes, 1
101		15 degree cold shock 10 minutes, 2
102		15 degree cold shock 10 minutes, 3
103		15 degree cold shock 10 minutes, 4
110	2	Acid Shock 1 min
111		Acid Shock 14 min
112		Acid Shock 20 min
113		Acid Shock 4 min
114		Acid Shock 8 min
115		Acid Shock Time 0, 1
116		Acid Shock Time 0, 2
120	3	Cipro20ng/ml Time 0
121		Cipro20ng/ml Time 1
122		Cipro20ng/ml Time 2
124		Cipro20ug/ml Time 0
125		Cipro20ug/ml Time 1
126		Cipro20ug/ml Time 2
127		Cipro20ug/ml Time 3
134	5	GrowthCurve Time 0
135		GrowthCurve Time 1
136		GrowthCurve Time 2
137		GrowthCurve Time 3
138		GrowthCurve Time 4
139		GrowthCurve Time 5
140	6	DH10B, LB
141		DH5alpha, LB
142		MG1655, LB, 1
143		MG1655, LB, 2
144		MG1655, Minimal Medium, Glucose, 37 degrees, 1
145		MG1655, Minimal Medium, Glucose, 37 degrees, 2
146		MG1655, Minimal Medium, Glucose, 37 degrees, 3
147		MG1655, Minimal Medium, Glucose, 37 degrees, 4
148		MG1655, Minimal Medium, Glucose, 37 degrees, 5
149		MG1655, Minimal Medium, Glucose, 37 degrees, 6
170	4	codB(b0336)::Tn5
172		crp(b3357)::Tn5
174		deaD(b3162)::Tn5, 1
175		deaD(b3162)::Tn5, 2
181		htrA(b0161)::Tn5
183		Multiple Deletions (MD12), 1
184		Multiple Deletions (MD12), 2
185		phoB(b0399)::Tn5
186		phoR(b0400)::Tn5
187		suhB(b2533)::Tn5, 1
188		suhB(b2533)::Tn5, 2
189		ydhB(b1659)::Tn5
190		yhaJ(b3105)::Tn5, 1
191		yhaJ(b3105)::Tn5, 2
192		yi52::Tn5, 1
193		yi52::Tn5, 2