Table 7. Top 5 networks for each comparison identified by Ingenuity pathway analysis using DE genes.

Comparison	Network	IPA Scorea	Genes
Infected versus non-infected mucosa	Cell Cycle, Reproductive System Development and Function, Cellular Movement	38	30
	Cell Cycle, DNA Replication, Recombination, and Repair, Cancer	36	29
	Cell Cycle, Cellular Assembly and Organization, DNA Replication, Recombination, and Repair	36	29
	Cell Death and Survival, Hematological System Development and Function, Cell Signaling	30	26
	Cell Signaling, Lipid Metabolism, Small Molecule Biochemistry	30	26
Infected versus non-infected lymph	Cancer, Organismal Injury and Abnormalities, Metabolic Disease	35	34
	Cancer, Organismal Injury and Abnormalities, Respiratory Disease	32	33
	Post-Translational Modification, Cell Cycle, Neurological Disease	32	33
	Post-Translational Modification, Amino Acid Metabolism, Small Molecule Biochemistry	30	32
	Dermatological Diseases and Conditions, Organismal Injury and Abnormalities, Antimicrobial Response	28	31
Resistant versus susceptible mucosa	Cellular Movement, Cellular Development, Embryonic Development	43	26
	Cardiovascular System Development and Function, Organismal Development, Cell-To-Cell Signaling and Interaction	36	23
	Cancer, Organismal Injury and Abnormalities, Cell Signaling	34	22
	Cellular Development, Connective Tissue Development and Function, Tissue Development	32	21
	Organ Morphology, Skeletal and Muscular System Development and Function, Tissue Morphology	27	19
Resistant versus susceptible lymph	Protein Synthesis, Molecular Transport, RNA Post-Transcriptional Modification	61	34
	Protein Synthesis, Gene Expression, RNA Post-Transcriptional Modification	40	26
	Antimicrobial Response, Inflammatory Response, Developmental Disorder	40	26
	Energy Production, Nucleic Acid Metabolism, Small Molecule Biochemistry	37	25
	Cancer, Endocrine System Disorders, Organismal Injury and Abnormalities	33	23

^a IPA network score is expressed as the -log (Fisher’s exact test p-value).