Table 3.

Top 20 most significantly overrepresented biological process gene ontology terms in downregulated differentially expressed genes when comparing mesenchymal stem cells (MSCs) exposed to activated peripheral blood mononuclear cells (PBMCs) from rheumatoid arthritis (RA) patients with MSCs exposed to resting PBMCs from RA patients

Category	Term	Genes in category	DEGs in category	p value	FDR p value
GO:0030198	Extracellular matrix organization	280	27	2.51E−11	7.88E−08
GO:0043062	Extracellular structure organization	280	27	2.51E−11	7.88E−08
GO:0032501	Multicellular organismal process	4070	128	1.65E−10	4.44E−07
GO:0007275	Multicellular organism development	3185	108	3.75E−10	7.84E−07
GO:0001501	Skeletal system development	357	28	8.09E−10	1.52E−06
GO:0044707	Single-multicellular organism process	3819	120	1.51E−09	2.36E−06
GO:0048731	System development	2834	98	1.77E−09	2.37E−06
GO:0009888	Tissue development	1147	54	2.54E−09	3.19E−06
GO:0048856	Anatomical structure development	3356	109	3.40E−09	4.00E−06
GO:0003008	System process	810	43	4.52E−09	5.00E−06
GO:0032502	Developmental process	3770	117	7.01E−09	7.33E−06
GO:0044767	Single-organism developmental process	3721	115	1.47E−08	1.46E−05
GO:0007155	Cell adhesion	890	44	2.26E−08	2.09E−05
GO:0022610	Biological adhesion	893	44	2.47E−08	2.09E−05
GO:0022617	Extracellular matrix disassembly	94	13	8.97E−08	6.49E−05
GO:0048513	Animal organ development	1980	72	1.20E−07	8.39E−05
GO:0030574	Collagen catabolic process	57	10	2.43E−07	1.63E−04
GO:0044243	Multicellular organism catabolic process	60	10	4.05E−07	2.54E−04
GO:0009653	Anatomical structure morphogenesis	1891	68	6.10E−07	3.59E−04
GO:0009887	Organ morphogenesis	617	32	1.76E−06	9.74E−04