Table 2 Summary of datasets used in the study

Boshoff et al.[37, 81]

Transcriptome profiling of M.tb under different combinations of drug treatment using whole genome microarrays.

(GSE1642 from GEO)

(transcriptome, FBA and network analysis)

KEGG [51]

Database for linking genomic, proteomic and pathway level information. Also hosts resources for metabolites and ligands.

(network analysis)

Reactome [85]

Open-source database for pathway information. It is manually curated and peer-reviewed.

(network analysis)

STRING [84]

Provides a list of protein-protein interactions based on computational, high-throughput experiments and literature survey.

(network analysis)

Wang et al.[86]

Protein – protein interactions were identified based on high-throughput bacterial two hybrid method.

(network analysis)

Vashisht et al.[34]

M.tb interactome pathway re-annotated and reconstructed, containing a total of 1434 proteins linked through 2575 functional relationship.

(network analysis)

Jamshidi et al.[45]

Reconstruction of metabolic network of the in silico strain of M.tb. Consists of 661 genes and 939 reactions. FBA was performed and essential genes were identified.

(FBA)

Fang et al.[48]

Reconstruction of metabolic network of the in silico strain of M.tb. Consists of 663 genes and 1049 reactions. FBA was performed and essential genes were identified.

Anand et al.[33]

Structural models were obtained and validated for 70% of the M.tb genome. Fold based functional annotations were assigned and novel binding sites identified.

(binding site analysis)

Sassetti et al.[18]

Transposon site hybridization was carried to identify set of essential genes.

(Validation)

Griffin et at.[16]

High density mutagenesis and deep sequencing carried out to identify essential genes.

(Validation)

Zhang et al.[19]

Identification of essential genes by dividing the whole genome sequence into windows of different length and performing TraSH analysis.