Table 2.

Summary of datasets used in the study

Dataset	Short description
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.