Computational protocol: Inactivation of Metabolic Genes Causes Short- and Long-Range dys-Regulation in Escherichia coli Metabolic Network

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Protocol publication

[…] Welch’s two sample T-tests were used to identify the significantly altered metabolites. R and Statistica data miner Version 10 were used for statistical analysis. Mole-file encoded chemical structures of the identified metabolites were retrieved from the PubChem database. A pair-wise Tanimoto chemical similarity matrix was calculated for the structures on the PubChem website. We downloaded the similarity matrix and used it as an input for MetaMapp software [] available at A single-step metabolic reaction network was calculated using KEGG RPAIR computations. Chemical similarity and KEGG RPAIR networks were merged into a single graph, which was visualized in Cytoscape. The Cytoscape Session file is provided in . […]

Pipeline specifications

Software tools Statistica, MetaMapp
Databases KEGG
Application Miscellaneous
Organisms Escherichia coli
Chemicals Carbon, Galactose, Glutathione, Nitrogen, Nucleotides