Table 1

Datasets used in this study

Reference

Short Description


Beste et al (2007) [20]

(GSMN-TB)

Reports GSMN-TB, a genome-scale metabolic model of Mtb, consisting of 849 unique reactions and 739 metabolites, and involving 726 genes. In silico gene deletions have been performed, using FBA, identifying genes essential for growth.

Jamshidi et al (2007) [19]

(Mtb iNJ661)

Reports the genome-scale metabolic reconstruction of the in silico strain Mtb iNJ661, comprising 661 genes and 939 reactions. In silico gene deletions have been performed, using FBA, identifying genes essential for growth, as well as slow-growing mutants.

Raman et al (2005) [21]

(MAP)

Reports an FBA of the mycolic acid pathway (MAP) in Mtb, comprising 217 reactions involving 197 metabolites and mediated by 28 proteins. In silico gene deletions have been performed, detailing genes essential for mycolic acid biosynthesis.

Sassetti et al (2003) [23]

(TraSH)

Reports the use of transposon site hybridisation (TraSH) mutagenesis to comprehensively identify the genes required by Mtb for optimal growth.

ModBase [25]

A database of structural models of proteins from various organisms, including Mtb and Human, based on homology modelling

Gao et al (2005) [30]

(Gao-expression)

Reports the variability in gene expression patterns among ten clinical isolates of Mtb, as well as the laboratory strains H37Rv and H37Ra, growing in liquid culture.

Rachman et al (2006) [31]

(Rxsachman-expression)

Reports genome-wide expression analysis of Mtb from clinical lung samples, as well as in vitro.

Boshoff et al (2004) [32]

(Boshoff-expression)

Reports gene expression of Mtb in response to several drugs/inhibitors of metabolism, as well as under persistence, starvation and different pH/media.

Muttucumaru et al (2004) [40]

(Muttucumaru-expression)

Reports global gene expression in aerobic, microaerophilic and anaerobic cultures.

Voskuil et al (2004) [39]

(Voskuil-expression)

Reports a genome expression profiling, analysing the adaptive mechanisms initiated by Mtb in two common models of Mtb non-proliferation.

Betts et al (2002) [38]

(Betts-expression)

Reports the use of gene and protein expression profiling to identify the response of Mtb to nutrient starvation, also modeling persistence.

Hampshire et al (2004) [41]

(Hampshire-expression)

Reports the stationary phase gene expression of Mtb following a progressive nutrient depletion, proposing a model for persistence.


Raman et al. BMC Systems Biology 2008 2:109   doi:10.1186/1752-0509-2-109

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