Strain-specific host gene networks activated in Mtb -infected BMM. Significantly differentially expressed host genes upon infection by CDC1551 or HN878 of BMM at 6 and 24 hpi were used to construct strain-specific networks by IPA. (A) Early immune activation network (EIAN); genes in this network were significantly up-regulated only in CDC1551 infected BMM at 6 hours. (B) Insignificant expression of EIAN genes during HN878 infection of BMM at 6 hours. (C and D) A subset of lipid metabolism pathway genes significantly activated only in HN878 infected BMM at 24 hours. (D) The majority of genes in the lipid metabolism pathway were not significantly expressed during CDC1551 infection of BMM at 24 hours. Up-regulated genes are marked red and down-regulated genes are marked green with their absolute level of expression under respective gene symbols (also described in Additional file 3). Solid lines indicate direct interaction and broken lines represent indirect interaction between the genes in the network.