Table 2 Top 20 most significantly overrepresented biological process gene ontology terms in upregulated differentially expressed genes when comparing the bone marrow mesenchymal stem cells (BM-MSCs) exposed to activated peripheral blood mononuclear cells (PBMCs) from rheumatoid arthritis patients vs. BM-MSCs exposed to resting PBMCs from RA patients

GO:0006955

Immune response

6.66E−65

1.25E−60

GO:0006952

Defense response

4.23E−62

3.98E−58

GO:0002376

Immune system process

2.41E−55

1.51E−51

GO:0043207

Response to external biotic stimulus

1.46E−46

5.49E−43

GO:0051707

Response to other organism

1.46E−46

5.49E−43

GO:0034097

Response to cytokine

2.84E−46

8.92E−43

GO:0071345

Cellular response to cytokine stimulus

3.89E−45

1.05E−41

GO:0009607

Response to biotic stimulus

1.35E−44

3.19E−41

GO:0006954

Inflammatory response

2.48E−44

5.19E−41

GO:0019221

Cytokine-mediated signaling pathway

1.70E−43

3.19E−40

GO:0002684

Positive regulation of immune system process

5.97E−40

1.02E−36

GO:0050896

Response to stimulus

7.48E−40

1.17E−36

GO:0002682

Regulation of immune system process

7.82E−38

1.13E−34

GO:0009605

Response to external stimulus

1.10E−35

1.38E−32

GO:0045087

Innate immune response

1.70E−35

1.99E−32

GO:0034341

Response to interferon-gamma

3.07E−33

3.04E−30

GO:0009617

Response to bacterium

5.57E−33

5.25E−30

GO:0006950

Response to stress

3.03E−32

2.72E−29

GO:0007154

Cell communication

1.14E−29

9.35E−27

GO:0001775

Cell activation

1.66E−29

1.24E−26