Table 1 KEGG pathways enriched in murine macrophages at 4 hpi. KEGG pathway analysis using ConsensusPathDB [58] identified signaling and metabolic pathways that were over-represented in L. major-infected mouse macrophages at 4 hpi (P value < 0.01) relative to uninfected controls. Genes that were differentially expressed (DE) by more than 2-fold were used as input with up- and downregulated genes considered separately. For each enriched KEGG pathway, the number of DE genes assigned to that pathway, the total number of genes in the pathway, and the P value for the enrichment are reported. The differentially expressed genes corresponding to each enriched KEGG pathway are reported in Additional file 4

KEGG pathway, upregulated

Number DE Genes

Pathway Size

P Value

  Cytokine-cytokine receptor interaction

  TNF signaling pathway

  Transcriptional misregulation in cancer

  HIF-1 signaling pathway

  Hematopoietic cell lineage

  NF-kappa B signaling pathway

  Jak-STAT signaling pathway

  Legionellosis

  PI3K-Akt signaling pathway

  MAPK signaling pathway

  Salmonella infection

  Malaria

  NOD-like receptor signaling pathway

  Rheumatoid arthritis

  Glycolysis/Gluconeogenesis

  Mineral absorption

  ECM-receptor interaction

  Tuberculosis

  Gap junction

  Axon guidance

  Arginine and proline metabolism

  Prion diseases

KEGG pathway, downregulated

Number DE Genes

Pathway Size

  Osteoclast differentiation

  Terpenoid backbone biosynthesis

  Staphylococcus aureus infection

  Steroid biosynthesis

  NOD-like receptor signaling pathway

  Peroxisome

  PPAR signaling pathway

  Chagas disease (American trypanosomiasis)

  Biosynthesis of unsaturated fatty acids

  Leishmaniasis

  ABC transporters

  Axon guidance

  Leukocyte transendothelial migration

  Fc gamma R-mediated phagocytosis

  Pancreatic cancer