The common pathways of upregulated genes in CD-inflammatory and UC-inflammatory samples were compared with CD- and UC-normal samples; these included: (1) Adaptive immunity: IBD; (2) Signal transduction: NF-kappa B signaling, TNF signaling, JAK-STAT signaling, and cytokine-cytokine receptor interaction; (3) Adhesion and differential: hematopoietic cell lineage and osteoclast differentiation; and (4) Autoimmune disease-related rheumatoid arthritis. Here, TNF is linked to inflammatory bowel disease.