Table 1 Summary of PROM, IDREAM, and PRIME model features.

Mtb model features	MTBPROM1.0¹¹	MTBPROM2.0¹²	PROM^a	PROM^a (EGRIN-PD)	IDREAM^b	PRIME
Metabolic model	iNJ661	iSM810	iEK1011	iEK1011	iEK1011	iEK1011
Number of reactions	1025	938	1229	1229	1229	1229
Number of metabolic genes in the metabolic network	661	810 (759 genes in iEK1011)	1011	1011	1011	1011
Regulatory network	Balazsi 2008	Minch 2015	Minch 2015	EGRIN-PD^c	EGRIN^c by Elastic net (FDR < 0.25)	EGRIN^c by Bayesian regression (Precision = 50%)
Number of transcription factors	30	104	104	131	142	142
Number of interactions	218	2555	2555	2410	3643	4820
Number of genes in the regulatory network (metabolic / total)	178/178	647/647	605/647	650/1509	641/2487	750/2905

Chandrasekaran et al.¹¹, Ma et al.¹².
^aThe PROM model was updated in this study by incorporating the latest MN model for Mtb.
^bThe IDREAM model was constructed for Mtb in this study to evaluate performance relative to the other methods.
^cPlease see Supplementary Fig. 4 for the differences in the EGRIN models derived using Inferelator.

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