Assays

Investigation of all steady state pH-values between pH 5.7 and 4.5 (pH 5.5, 5.3, 5.1, 4.9, 4.7).

Comparison of the transcriptome at steady state in acidogenesis and at steady state in solventogenesis.

Investigation of the dynamic switch at pH values between 5.8 and 4.5 (pH 5.5, 5.3, 5.1, 4.9, 4.7 and 4.5).

Contributor: Sara Jabbari

Assay type: Genomics

Technology type: Microarray

Snapshots: No snapshots

Cytoscape based analysis and yED based representation of clostridial Reactomes

Contributor: Sebastian Curth

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Using PCA, three components, beam size 8.
Clustering via MCL from Biolayout Express 3D

Data is taken from "Genome-Wide Gene Expression Analysis of the Switch between Acidogenesis and Solventogenesis in Continuous Cultures of Clostridium acetobutylicum." Grimmler et al. 2011
DOI: 10.1159/000320973

Contributor: Sebastian Curth

Biological problem addressed: Gene Expression

Snapshots: No snapshots

No description specified

Contributor: Sebastian Curth

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Using Taverna for mining and MATLAB for conversion into specific formats (cytoscape, SBTOOLBOX2)

Steady state study of the effect of altering gene regulation on yields of end-products, focusing on butanol.

Contributor: Sara Jabbari

Biological problem addressed: Gene Expression

Snapshots: No snapshots

Measurements of acetone, butanol, acetate, butyrate and ethanol taken during dynamic shift (pH 5.8, 5.5, 5.3, 5.1, 4.9, 4.7, 4.5) and at steady state (pH 5.7, 5.5, 5.3, 5.1, 4.9, 4.7, 4.5).

No description specified

Contributor: John Raedts

Assay type: Metabolomics

Technology type: Technology Type

Snapshots: No snapshots

Time-dependent simulations of the dynamic switch between acidogenesis and solventogenesis based on the metabolic network and pH-dependent regulation of the enzymes.

Contributor: Sara Jabbari

Biological problem addressed: Metabolic Network

Snapshots: No snapshots

No description specified
No description specified

Contributor: Sebastian Curth

Assay type: Transcriptional Profiling

Technology type: Microarray

Snapshots: No snapshots

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