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Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera

Tom A Mendum, Jane Newcombe, Ahmad A Mannan, Andrzej M Kierzek and Johnjoe McFadden*

Author Affiliations

Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK

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Genome Biology 2011, 12:R127  doi:10.1186/gb-2011-12-12-r127

Published: 30 December 2011

Additional files

Additional file 1:

Nmb_iTM560 model. An Excel file containing the Nmb_iTM560 model, metabolites, substrate conditions, stoichiometries and the original iAF1260 model of E. coli K12 [22].

Format: XLS Size: 1.4MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Nmb_iTM560 biomass calculations. An Excel file containing calculations to determine biomass components and stoichiometries, and molecular weights using data from the iAF1260 model of E. coli K12 [22] modified with N. meningitidis-specific data [19,25,26]

Format: XLS Size: 120KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Flux variable analysis. An Excel file containing maximal and minimal reaction fluxes compatible with maximal flux to biomass were computed for minimal media agar and serum.

Format: XLS Size: 631KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Nmb_iTM560 predicted essential genes. An Excel file containing lists of essential genes predicted by flux balance analysis. Individual genes were removed from the model and maximal possible growth rate determined. In silico gene knockouts that gave maximal fluxes to the biomass (the essential version) of approximately zero were considered essential.

Format: XLS Size: 690KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Microarray data and analysis for known mutants, assessment of bias in data and ROC analysis. An Excel file containing TraSH data for mixes of known mutants, an assessment of bias within the TraSH data and receiver operating characteristic (ROC) analysis.

Format: XLS Size: 570KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Analyses of TraSH microarray data grouped by growth condition. An Excel file containing TraSH data. Data are grouped by growth condition.

Format: XLS Size: 1.9MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Analyses of TraSH microarray data grouped by functionality. An Excel file containing TraSH data. Data are grouped by functionality.

Format: XLS Size: 3.7MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data