Table 2.

Gene ontology (GO) analysis with the 87 transcripts dysregulated between responders and non-responders to abatacept/methotrexate

GO accession	GO term	P value	Count in 87 mRNA list	Percentage in 87 mRNA list	Count in human genome	Percentage in human genome	Enrichment
Biological process
GO:1902600	Hydrogen ion transmembrane transport	0.0011	6	10.17	93	0.55	18.38
GO:0022904	Respiratory electron transport chain	0.0011	6	10.17	99	0.59	17.26
GO:0022900	Electron transport chain	0.0011	6	10.17	101	0.60	16.92
GO:0045333	Cellular respiration	0.0011	7	11.86	146	0.87	13.66
GO:0015992	Proton transport	0.0019	6	10.17	115	0.68	14.86
GO:0006818	Hydrogen transport	0.0019	6	10.17	117	0.70	14.61
Molecular function
GO:0015002	Heme-copper terminal oxidase activity	0.0011	4	6.78	23	0.14	49.54
GO:0004129	Cytochrome-c oxidase activity	0.0011	4	6.78	23	0.14	49.54
GO:0016676	Oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor	0.0011	4	6.78	23	0.14	49.54
GO:0016675	Oxidoreductase activity, acting on a heme group of donors	0.0011	4	6.78	24	0.14	47.47
GO:0015078	Hydrogen ion transmembrane transporter activity	0.0011	6	10.17	88	0.52	19.42
Cellular localization
GO:0070469	Respiratory chain	0.0011	6	10.17	68	0.40	25.13
GO:0044455	Mitochondrial membrane part	0.0011	7	11.86	144	0.86	13.85
GO:0005743	Mitochondrial inner membrane	0.0011	10	16.95	350	2.08	8.14
GO:0019866	Organelle inner membrane	0.0011	10	16.95	390	2.32	7.30
GO:0005746	Mitochondrial respiratory chain	0.0017	5	8.47	62	0.37	22.97
GO:0005740	Mitochondrial envelope	0.0017	11	18.64	544	3.24	5.76
GO:0031966	Mitochondrial membrane	0.0053	10	16.95	508	3.02	5.61

Corrected p values were determined by a standard hypergeometric distribution