Table 2.

Ingenuity pathway analysis (IPA)

Top canonical pathways
Name	p value	Overlap
Altered T cell and B cell signalling in rheumatoid arthritis	1.41E− 10	17.3%, 14/81
TREM1 signalling	2.53E− 10	18.6%, 13/70
Dendritic cell maturation	5.68E− 08	9.5%, 16/169
Allograft rejection signalling	1.39E− 07	18.8%, 9/48
Communication between innate and adaptive immune cells	2.06E− 07	13.4%, 11/82
Top upstream regulators
Upstream regulator	p value of overlap
TGM2	4.66E− 15
CEBPA	1.16E− 08
CSF2	1.70E− 08
TNF	1.53E− 06
IRF4	2.33E− 06
Top diseases and disorders
Name	p value	Molecules
Immunological disease	6.30E− 03 to 1.20E− 22	151
Connective tissue disorders	5.32E− 03 to 3.31E− 21	81
Inflammatory disease	6.18E− 03 to 3.31E− 21	116
Skeletal and muscular disorders	5.32E− 03 to 3.31E− 21	106
Infectious diseases	5.76E− 03 to 5.84E− 20	76
Top molecular and cell functions
Name	p value	Molecules
Cell-to-cell signalling and interaction	6.18E− 03 to 1.99E− 14	100
Cell death and survival	7.09E− 03 to 3.79E− 10	97
Cellular movement	6.44E− 03 to 4.26E− 10	55
Cellular development	6.48E− 03 to 5.54E− 10	49
Cellular growth and proliferation	6.18E− 03 to 5.54E− 10	84
Top physiological system development and function
Name	p value	Molecules
Haematological system development and function	6.48E− 03 to 6.44E− 13	72
Immune cell trafficking	6.18E− 03 to 6.44E− 13	47
Embryonic development	1.86E− 05 to 1.86E− 05	4
Haematopoiesis	6.48E− 03 to 2.86E− 05	24
Hair and skin development and function	6.18E− 03 to 4.26E− 05	10

The differentially expressed genes in adalimumab good-responders (baseline versus 3 months) were analysed using Ingenuity Pathway Analysis (IPA) software. The top associated terms for the output themes, which were either up- or downregulated, are presented with associated p values. The table also displays the number of molecules, or the number of differentially expressed transcripts within the dataset associated with each term