Identification of clusters of co-regulated and anti-regulated genes
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Provided with genomic data over different pH values we have the opportunity to study the similarity of gene expression profiles and cluster groups of very simlar gene expression profiles. Via PCA we can furthermore study dynamic similarity and compe genes that are possible co-regulators or anti-regulators in the clostridial metabolism.
SEEK ID: https://fairdomhub.org/studies/71
The effect of pH upon the metabolic shift in Clostridium acetobutylicum in continuous culture.
Projects: COSMIC
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Created: 3rd Nov 2011 at 14:29
Last updated: 22nd Nov 2011 at 19:12
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Projects: COSMIC
Institutions: Beuth University of Applied Sciences Berlin
I am a biotechnologist with main focus on theoretical studies. Currently, I am working on the implementation of a parameter estimation algorithm on GPUs to reduce the computational burden of huge ODE systems. I am a PAL and I am looking forward to communication with other SYSMO members.
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep
Web page: http://sysmo.net/
Systems Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=54
Submitter: Christina Döring
Studies: Effect of pH on the metabolome, Effect of pH on the proteome, Effect of pH upon the transcriptome, Identification of clusters of co-regulated and anti-regulated genes, Modelling the effect of pH on the metabolic shift
Assays: Comparison of the proteome between pH 5.7 (acidogenesis) and pH 4.5 (sol..., Comparison of the transcriptome between pH 5.7 (acidogenesis) and pH 4.5..., Comparison of the transcriptome between pH 5.8 (acidogenesis) and pH 4.5..., Identification of dynamically similar transcript profiles, Steady state study of the effect of gene regulation on yields of end-pro..., Study of the end products of the acidogenesis and solventogenesis pathways, Time-dependent simulations
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
Submitter: Sebastian Curth
Biological problem addressed: Gene Expression
Investigation: The effect of pH upon the metabolic shift in Cl...
