Table 2:

Most up-regulated canonical pathways, determined by IPA

Canonical Biologic Pathway	No. of Genes Up-Regulated	Genes	No. of Genes Down-Regulated	Gene(s)
Dendritic cell maturation	25	CD80, CD83, CD86, CD1C, COL10A1, COL1A1, COL1A2, FCGR1B, FCGR2A, HLA-A, HLA-DMA, HLA-DMB, HLA-DOB, HLA-DQA1, HLA-DRA, HLA-DRB1, HLA-DRB5, IL15, IL1B, IL1RL2, IL1RN, PIK3CG, PIK3R5, PLCB2, TREM2	3	CREB5, PLCB4, PLCL1
Role of NFAT in regulation of the immune response	22	BLNK, BTK, CD80, CD86, FCER1A, FCGR1B, FCGR2A, FOS, GNG2, HLA-DMA, HLA-DMB, HLA-DOB, HLA-DQA1, HLA-DRA, HLA-DRB1, HLA-DRB5, LCP2, LYN, PIK3CG, PIK3R5, PLCB2, SYK	2	PLCB4, GNAO1
Antigen-presentation pathway	12	CD74, HLA-A, HLA-DMA, HLA-DMB, HLA-DOB, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB2, HLA-DRA, HLA-DRB1, HLA-DRB5	0	NA
Altered T-cell and B-cell signaling in rheumatoid arthritis	17	CCL21, CD80, CD86, HLA-DMA, HLA-DMB, HLA-DOB, HLA-DQA1, HLA-DRA, HLA-DRB1, HLA-DRB5, IL15, IL1B, IL1RN, SPP1, TLR1, TLR8, TNFSF13B	0	NA
Atherosclerosis signaling	19	ALOX5, CCL2, CCR2, COL10A1, COL1A1, COL1A2, CXCR4, IL8, IL1B, IL1RN, LYZ, MSR1, PDGFB, PDGFC, PDGFD, PLA2G7, PLA2R1, SELE, VCAM1	1	RBP4

Note:—NA indicates not applicable; NFAT, nuclear factor of activated T cells.