Elementary mode analysis and metabolic flux analysis of L-glutamate biosynthesis byCorynebacterium glutamicum

2009 ◽  
Vol 59 (2) ◽  
pp. 317-322 ◽  
Author(s):  
Ning Chen ◽  
Jun Du ◽  
Hui Liu ◽  
Qingyang Xu
Keyword(s):  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Mode Analysis ◽  
Flux Analysis ◽  
Elementary Mode ◽  
Elementary Mode Analysis ◽  
Glutamate Biosynthesis

scholarly journals Principal Metabolic Flux Mode Analysis

2017 ◽  
Author(s):  
Sahely Bhadra ◽  
Peter Blomberg ◽  
Sandra Castillo ◽  
Juho Rousu
Keyword(s):  
Metabolic Flux ◽  
Principal Component ◽  
Supplementary Information ◽  
Mode Analysis ◽  
Flux Analysis ◽  
Large Set ◽  
Elementary Mode Analysis ◽  
Modes Of Variability ◽  
Link Type ◽  
Flux Mode

AbstractMotivationIn the analysis of metabolism using omics data, two distinct and complementary approaches are frequently used: Principal component analysis (PCA) and Stoichiometric flux analysis. PCA is able to capture the main modes of variability in a set of experiments and does not make many prior assumptions about the data, but does not inherently take into account the flux mode structure of metabolism. Stoichiometric flux analysis methods, such as Flux Balance Analysis (FBA) and Elementary Mode Analysis, on the other hand, produce results that are readily interpretable in terms of metabolic flux modes, however, they are not best suited for exploratory analysis on a large set of samples.ResultsWe propose a new methodology for the analysis of metabolism, called Principal Metabolic Flux Mode Analysis (PMFA), which marries the PCA and Stoichiometric flux analysis approaches in an elegant regularized optimization framework. In short, the method incorporates a variance maximization objective form PCA coupled with a Stoichiometric regularizer, which penalizes projections that are far from any flux modes of the network. For interpretability, we also introduce a sparse variant of PMFA that favours flux modes that contain a small number of reactions. Our experiments demonstrate the versatility and capabilities of our methodology.AvailabilityMatlab software for PMFA and SPMFA is available in https://github.com/ aalto-ics-kepaco/[email protected], [email protected], [email protected], [email protected] informationDetailed results are in Supplementary files. Supplementary data are available at https://github.com/aalto-ics-kepaco/PMFA/blob/master/Results.zip.

scholarly journals Integration of enzyme activities into metabolic flux distributions by elementary mode analysis

2007 ◽  
Vol 1 (1) ◽  
Author(s):  
Hiroyuki Kurata ◽  
Quanyu Zhao ◽  
Ryuichi Okuda ◽  
Kazuyuki Shimizu
Keyword(s):  
Enzyme Activities ◽  
Metabolic Flux ◽  
Mode Analysis ◽  
Elementary Mode ◽  
Elementary Mode Analysis

13C metabolic flux analysis in cell line and bioprocess development

2021 ◽  
Vol 34 ◽  
pp. 100718
Author(s):  
Sarah A Sacco ◽  
Jamey D Young
Keyword(s):  
Cell Line ◽  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Flux Analysis ◽  
Bioprocess Development ◽  
13C Metabolic Flux Analysis

The benefits of being transient: isotope-based metabolic flux analysis at the short time scale

2011 ◽  
Vol 91 (5) ◽  
pp. 1247-1265 ◽  
Author(s):  
Katharina Nöh ◽  
Wolfgang Wiechert
Keyword(s):  
Metabolic Flux Analysis ◽  
Time Scale ◽  
Metabolic Flux ◽  
Short Time Scale ◽  
Flux Analysis ◽  
Short Time

scholarly journals Metabolic Flux Analysis of the Phenylpropanoid Pathway in Wound-Healing Potato Tuber Tissue using Stable Isotope-Labeled Tracer and LC-MS Spectroscopy

2003 ◽  
Vol 44 (9) ◽  
pp. 961-961 ◽  
Author(s):  
Fumio Matsuda ◽  
Keiko Morino ◽  
Masahiro Miyashita ◽  
Hisashi Miyagawa
Keyword(s):  
Wound Healing ◽  
Stable Isotope ◽  
Potato Tuber ◽  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Phenylpropanoid Pathway ◽  
Flux Analysis ◽  
Tuber Tissue ◽  
Potato Tuber Tissue
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