Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks

2004 ◽  
Vol 86 (3) ◽  
pp. 251-260 ◽  
Author(s):  
Tunahan Çakir ◽  
Betül Kirdar ◽  
Kutlu Ö. Ülgen
Keyword(s):  
Pathway Analysis ◽  
Metabolic Pathway ◽  
Metabolic Networks ◽  
Metabolic Pathway Analysis

scholarly journals Scalable metabolic pathway analysis

2020 ◽  
Author(s):  
Ove Øyås ◽  
Jörg Stelling
Keyword(s):  
Pathway Analysis ◽  
Metabolic Pathway ◽  
Large Scale ◽  
Metabolic Networks ◽  
Central Carbon Metabolism ◽  
Graph Representation ◽  
Metabolic Pathway Analysis ◽  
A Genome ◽  
Scope Of Application ◽  
Genome Scale

The scope of application of genome-scale constraint-based models (CBMs) of metabolic networks rapidly expands toward multicellular systems. However, comprehensive analysis of CBMs through metabolic pathway analysis remains a major computational challenge because pathway numbers grow combinatorially with model sizes. Here, we define the minimal pathways (MPs) of a metabolic (sub)network as a subset of its elementary flux vectors. We enumerate or sample them efficiently using iterative minimization and a simple graph representation of MPs. These methods outperform the state of the art and they allow scalable pathway analysis for microbial and mammalian CBMs. Sampling random MPs from Escherichia coli’s central carbon metabolism in the context of a genome-scale CBM improves predictions of gene importance, and enumerating all minimal exchanges in a host-microbe model of the human gut predicts exchanges of metabolites associated with host-microbiota homeostasis and human health. MPs thereby open up new possibilities for the detailed analysis of large-scale metabolic networks.

scholarly journals PySCeSToolbox: a collection of metabolic pathway analysis tools

2017 ◽  
Vol 34 (1) ◽  
pp. 124-125 ◽  
Author(s):  
Carl D Christensen ◽  
Jan-Hendrik S Hofmeyr ◽  
Johann M Rohwer
Keyword(s):  
Pathway Analysis ◽  
Metabolic Pathway ◽  
Metabolic Pathway Analysis ◽  
Analysis Tools

Toward Genome-Scale Metabolic Pathway Analysis

2016 ◽  
pp. 111-123 ◽  
Author(s):  
Jürgen Zanghellini ◽  
Matthias P. Gerstl ◽  
Michael Hanscho ◽  
Govind Nair ◽  
Georg Regensburger ◽  
...  
Keyword(s):  
Pathway Analysis ◽  
Metabolic Pathway ◽  
Metabolic Pathway Analysis ◽  
Genome Scale
Sign in / Sign up

Export Citation Format

Share Document