40 samples internal metabolite concentrations FC values used for model simmulations Version 1
ExploreContains relative metabolite concentrations for 40 samples based on technical triplicates. Medium and SD values were calculated and used for 1000 sampled simmulations (sampling from the measurement distribution per metabolite) per sample.
Also contains annotion to link metabolite concentrations and protein fold change measurements for OE and KO mutants to the model as well as external glucose, acetate and lactate concentrations. A SBtab like format was used to easily load the MEAN and SD metabolite concentration data with metadata for samples and metabolite in a custom simmulation pipeline.
SEEK ID: https://fairdomhub.org/data_files/2328?version=1
Filename:
40_Independend_samples.xlsx
Format: Spreadsheet
Size: 1.02 MB
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Views: 391 Downloads: 7
Created: 7th Jan 2019 at 15:32
Last updated: 14th Jan 2019 at 16:00
Last used: 20th Oct 2019 at 18:29
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https://orcid.org/0000-0001-7049-5334I am a researcher (PhD student) working at Wageningen University & Research as bioinformatician and modeller. I am working as part of the MycoSynVac (http://www.mycosynvac.eu/) project on dynamic modelling of central carbon metabolism in M. pneumoniae, to be extended to full dynamic modelling of metabolism to be implemented in a whole cell model.
I am also looking into possibilities to improve standards in model generation using semantic technologies, improving automatic generation, annotation
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The MycoSynVac project AIMS at using cutting-edge synthetic biology methodologies to engineer Mycoplasma pneumoniae as a universal chassis for vaccination.
Designing a universal Mycoplasma chassis that can be deployed as single- or multi-vaccine in a range of animal hosts. Annually, infections caused by Mycoplasma species in poultry, cows, and pigs result in multimillion Euro losses in the USA and Europe.
There is no effective vaccination against many Mycoplasmas that infect pets, humans and farm
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Programme: Independent Projects
Public web page: http://www.mycosynvac.eu/
Contains the analysis of the internal metabolite concentrations of the 40 independend samples
Pearson correlation was used to generate heatmaps
Pearson correlation with p-value cutof of 0.001 was used and as input for a correlation network (grouping using H-clust)
Principal component analysis was performed on samples, F-ion and H-ion data combined and seperately
Zip files contains the data (FC.txt), PCA and heatmap plots and the script to re-generate these plots
Contributor: Niels Zondervan
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
