Table 2 Top Pathways enriched in the DEGs specific to RA compared to healthy and OA

GO Biological Processes

GO:0098542

defense response to other organism

BIRC3, GBP1, IGHD, IGHM, IGKC, CXCL10, MICB, CXCL9, STAT1, AIM2, CXCL13, IGHV3–7, TRBC1, IGKV3–20, SLAMF8, IGLL5, CCR5, CSF2RB, GZMA, PLCG2, CCL5, POU2AF1, IGKV4–1, LCK, PSMB9, CD2, LCP1, TPD52, IL21R, TAP1, LAMP3, IGKV1D-13, IL2RG

GO Biological Processes

GO:0050900

leukocyte migration

CD2, CCR5, IGHM, IGKC, CXCL10, LCK, CXCL9, CCL5, CCL18, CXCL13, IGHV3–7, IGKV4–1, IGKV3–20, SLAMF8, CSF2RB, IL2RG, IL21R, STAT1, PLCG2, SLC39A8, SEMA4D, PLEKHO1, FAM20B, ADAMDEC1, GABBR1, AIM2, BIRC3, NCOR2, GBP1

GO Biological Processes

GO:0019221

cytokine-mediated signaling pathway

BIRC3, CCR5, CSF2RB, GBP1, IL2RG, CXCL10, LCP1, CXCL9, PSMB9, CCL5, CCL18, STAT1, IL32, AIM2, CXCL13, IL21R, LCK

Reactome Gene Sets

R-HSA-451927

Interleukin-2 family signaling

CSF2RB, IL2RG, LCK, STAT1, IL21R, CCR5, GZMA, TAP1

GO Biological Processes

GO:0009615

response to virus

BIRC3, GBP1, CXCL10, MICB, CXCL9, CCL5, STAT1, AIM2, PSMB9, CCL18, PLCG2, SLAMF8, LCK, LAMP3, CCR5, TAP1

GO Biological Processes

GO:0050852

T cell receptor signaling pathway

GBP1, LCK, PLCG2, PSMB9, TRBC1, CD2, TPD52, SLAMF8, BIRC3, STAT1, MICB

GO Biological Processes

GO:0050922

negative regulation of chemotaxis

SEMA4D, CXCL13, SLAMF8, GBP1, LCK, CCL5, CYTIP, ADAMDEC1, CCL18, AIM2, TBC1D9, SLC39A8, CXCL10, PLCG2, MICB

GO Biological Processes

GO:0001819

positive regulation of cytokine production

BIRC3, CD2, IGHD, PLCG2, STAT1, AIM2, GBP1, CCL5, LCP1

GO Biological Processes

GO:0071347

cellular response to interleukin-1

GBP1, PSMB9, CCL5, CCL18, STAT1

GO Biological Processes

GO:0002474

antigen processing and presentation of peptide antigen via MHC class I

MICB, PSMB9, TAP1

GO Biological Processes

GO:0042110

T cell activation

CD2, LCK, LCP1, MICB, CCL5

GO Biological Processes

GO:1905330

regulation of morphogenesis of an epithelium

CXCL10, PSMB9, STAT1, LCK, NCOR2