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NOTIFICATION: Permanent migration of all CSB.DB services and functionalities on 1.1.2016.
Herewith we inform you that all CSB.DB databases have been migrated at the beginning of 2016. This includes all gene correlation and expression databases, the GMD@CSB.DB module and all associated databases
The BestFit software, a tool for non-aqueous fractionation data analysis, will also be available by the Experimental Systems Biology Research Group headed by Dr. Patrick Giavalisco.
We thank all users, contributors, and collaborators of CSB.DB at the Max Planck Institute for their long-standing support.
Yours sincerely, the CSB.DB Curator and the CSB.DB Developmental Core Team
Matrices@CSB.DB: E.coli Matrix Information Page
Matrix
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 smd4502 : Processing

Escherichia coli - Expression Data Matrix smd4502 (m4502): Processing back to top


Transcript profiles of Matrix smd4502 (m4502) were derived from the Stanford Microarray Database (SMD, Sherlock et al., 2001). Gene expression was analysed by colour-coded cDNA hybridisation technology. Experiments were mainly related to amino-acid metabolism (Khodursky et al., 2000), DNA metabolism (Courcelle et al., 2001), and RNA decay (Bernstein et al., 2002). Individual spots were quality checked as recommended by the SMD tutorial. In order to reduce the number of missing data smd4502 (m4502) was designed to maximise the number of genes, comprised 34 experiments, which were described by 1845 genes (Steinhauser et al., 2004a). Normalised gene expression ratios (Rat2N) were log base 2 transformed. Co-Response analyses were performed on range normalised (genes) matrix.
For detailed description of the experiments please query the Stanford Microarray Database (SMD). You can search for details via SMD.ID (Stanford Experiment ID), by Experimenter or Category etc.
Matrix smd4502: Experiments

Escherichia coli - Expression Data Matrix smd4502 (m4502): Experiment List back to top


For detailed description of the experiments please query the Stanford Microarray Database (SMD). You can search for details via SMD.ID (Stanford Experiment ID), by Experimenter or Category etc.
CSB.DB ID SMD.ID Group Description SMD Category SMD Sub-Category Experimenter
114 1641 2 60'+50ug/ml Trp vs 0' in min med +0.2% glu Amino Acid metabolism Tryptophan KHODURSK
119 5266 cy_b4
127 1639 30'+50ug/ml Trp vs 0' in min med +0.2% glu
129 1637 5'+50ug/ml Trp vs 0' in min med +0.2% glu
130 1597 60' vs 0' in minimal medium +0.2% glu, II
131 1595 30' vs 0' in minimal medium +0.2% glu
133 1592 5' vs 0' in minimal medium +0.2% glu
137 9395 60' vs 0' in minimal medium +0.2% glu
138 5265 cy_a4
147 1916 3 lexA vs. wt, before UV treatment, MG1655 DNA metabolism UV radiation KHODURSK
148 1909 lexA 60' after NOuv vs. 0', MG1655
149 1911 lexA 10' after UV vs. 0', MG1655
150 1912 lexA 20' after UV vs. 0', MG1655
151 1913 lexA 40' after UV vs. 0', MG1655
152 1915 lexA 60' after UV vs. 0', MG1655
153 1908 lexA 20' after NOuv vs. 0', MG1655
154 1914 lexA 5' after UV vs. 0', MG1655
210 8582 7 2' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B RNA decay Rifampicin JONB
213 8589 8' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B
214 8536 2' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial A
215 8538 4' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial A
217 8540 6' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial A
219 8586 6' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B
220 8542 8' RNA Decay of MG1655 (Repaired MCM 3416) in M9 + 0.2% Glucose Trial A
221 8584 4' RNA Decay of MG1655 (Repaired NCM 3416) in M9 + 0.2% Glucose Trial B
222 15336 N3433 (wt) vs N3433 (rne deletion) pBADRNE in LB at 30 degrees C Trial B * RNA JONB
223 13838 N3433 (wt) vs N3433 (rne deletion) pBAD-RNE w/out Arabinose in LB at 30 degrees Trial A
224 13840 N3433 (wt) vs N3433 (rng deletion) in LB at 30 degrees C Trial B
225 15343 N3433 (wt) vs N3433 (rng deletion) LB at 30 C Trial A *
227 15341 N3433 (wt) vs N3433 (rne deletion) pNRNE5 at 30 degrees C Trial A *
228 15340 N3433 (wt) vs N3433 (rne deletion) pRNG3 at 30 degrees C Trial B *
229 15339 N3433 (wt) vs N3433 (rne deletion) pRNG3 at 30 degrees C Trial A *
230 15338 N3433 (wt) vs N3433 (wt) pRNG3 in LB at 30 degrees Trial B *
231 15337 N3433 (wt) vs N3433 (wt) pRNG3 in LB at 30 degrees Trial A *

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