Table 4.

Supra-categories including the biological process gene ontology terms significantly overrepresented when comparing mesenchymal stem cells (MSCs) exposed to activated peripheral blood mononuclear cells (PBMCs) from rheumatoid arthritis (RA) patients vs. MSCs exposed to activated PBMCs from RA patients

Supra-category	Number of categories in upregulated genes	Number of categories in downregulated genes
Immune system-related	407	2
Signaling-related	89	0
Calcium metabolism-related	53	0
Development-related	50	18
Response to pathogens-related	45	0
Nucleic acids metabolism-related	18	0
Wound repair-related	12	0
Nitric oxide metabolism-related	6	0
Miscellanea	84	6