Table 4A.

Top 12 canonical pathways predicted from cluster X vs Y+Z differentially expressed genes

Ingenuity Canonical Pathways	Activation z-score	−log (p-value)
Phagosome Formation		14.1
Hepatic Fibrosis / Hepatic Stellate Cell Activation		12.7
Dendritic Cell Maturation	5.47	9.78
GP6 Signaling Pathway	4.70	8.46
Granulocyte Adhesion and Diapedesis		8.08
Neuroinflammation Signaling Pathway	4.90	7.38
Role of Macrophages, Fibroblasts and Endothelial Cells in Rheumatoid Arthritis		7.35
B Cell Receptor Signaling	4.27	7.21
Communication between Innate and Adaptive Immune Cells		7.18
Th2 Pathway	2.13	7.17
Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses	3.84	7.07
Altered T Cell and B Cell Signaling in Rheumatoid Arthritis		7.04

Top 12 based on p-value. For reference, −log(0.05/1000)=4.30, so all p-values shown in the table are statistically significant at level 0.05 even after a conservative Bonferroni correction for 1000 tests. The Ingenuity Pathway Analysis database lacked enough data to calculate activation z-scores for some canonical pathways. These are left blank.