Skip to main content

Advertisement

Table 3 Gene ontology terms that are enriched in two or more sets of genes

From: An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype

Comparison name   Combined OA+NL OA or NL
Comparison description   RA vs OA or NL or OA+NL RA vs OA+NL RA vs OA or NL
Pathway name GO type EF ( q -value) # of DMGs (%) EF ( q -value) # of DMGs (%) EF ( q -value) # of DMGs (%)
positive regulation of ERK1 and ERK2 cascade BP 3.5 (0.000494) 18 (38.3) 9.0 (0.000111) 9 (19.1) 3.3 (0.00106) 17 (36.2)
proteinaceous extracellular matrix CC 2.2 (7.07e-05) 48 (24.2) 3.3 (0.00287) 14 (7.1) 2.1 (0.000254) 46 (23.2)
signal transduction BP 1.4 (0.000717) 174 (15.4) 1.5 (0.0263) 37 (3.3) 1.4 (0.000713) 172 (15.2)
extracellular matrix CC 2.3 (0.00282) 30 (25.0) 2.3 (0.0441) 6 (5.0) 2.3 (0.00192) 30 (25.0)
inflammatory response BP 1.8 (0.00821) 45 (20.1) 2.3 (0.0301) 11 (4.9) 1.8 (0.0106) 44 (19.6)
fibroblast growth factor receptor signaling' BP 9.1 (0.02) 4 (100.0) 23.5 (0.0176) 2 (50.0) 9.2 (0.0177) 4 (100.0)
MHC class II protein complex CC 4.5 (0.0346) 7 (50.0) 20.1 (9.47e-05) 6 (42.9) 4.6 (0.0303) 7 (50.0)
focal adhesion CC 2.1 (0.0176) 26 (23.6) 2.6 (0.0418) 6 (5.5) 2.2 (0.0136) 26 (23.6)
Rho guanyl-nucleotide exchange factor activity MF 2.3 (0.0443) 18 (25.4) 3.3 (0.0375) 5 (7.0) 2.3 (0.0377) 18 (25.4)
regulation of Rho protein signal transduction BP 2.3 (0.0481) 18 (25.0) 3.3 (0.038) 5 (6.9) 2.3 (0.0412) 18 (25.0)
positive regulation of inflammatory response BP 3.3 (0.0173) 12 (36.4)    3.3 (0.0141) 12 (36.4)
cell adhesion BP 1.4 (0.0425) 84 (15.7)    1.4 (0.0404) 83 (15.5)
extracellular region CC 1.6 (2.4e-13) 306 (17.2) 1.8 (0.000356) 67 (3.8) 1.6 (4.11e-13) 302 (16.9)
extracellular space CC 1.6 (2.91e-06) 133 (18.1) 2.2 (0.000971) 34 (4.6) 1.6 (7.7e-06) 130 (17.7)
immune response BP 1.9 (0.000153) 64 (21.0) 3.1 (0.000722) 20 (6.6) 1.9 (0.000352) 62 (20.3)
plasma membrane CC 1.3 (4.6e-08) 467 (14.3) 1.4 (0.00269) 99 (3.0) 1.3 (6.35e-08) 461 (14.1)
Z disc CC 3.5 (0.00133) 16 (38.1) 5.6 (0.0161) 5 (11.9) 3.5 (0.00099) 16 (38.1)
scavenger receptor activity MF 3.5 (0.00104) 16 (39.0) 4.6 (0.0327) 4 (9.8) 3.6 (0.000814) 16 (39.0)
odontogenesis BP 4.2 (0.00175) 12 (46.2) 5.4 (0.0374) 3 (11.5) 4.2 (0.00132) 12 (46.2)
integral to plasma membrane CC 1.4 (0.00501) 149 (15.2) 1.6 (0.0271) 33 (3.4) 1.4 (0.0102) 145 (14.8)
multicellular organismal development BP 1.5 (0.000606) 143 (16.1) 1.4 (0.0435) 27 (3.0) 1.5 (0.000332) 143 (16.1)
structural molecule activity MF 1.9 (0.00594) 42 (20.9) 2.1 (0.0414) 9 (4.5) 1.9 (0.0041) 42 (20.9)
positive regulation of cell proliferation BP 1.6 (0.019) 58 (17.8) 2.9 (0.00105) 20 (6.2) 1.6 (0.0315) 56 (17.2)
positive regulation of interferon-gamma production BP 3.2 (0.0439) 10 (35.7) 10.1 (0.00104) 6 (21.4) 3.3 (0.0383) 10 (35.7)
skeletal muscle contraction BP 5.5 (0.0292) 6 (60.0) 9.4 (0.0378) 2 (20.0) 5.5 (0.0256) 6 (60.0)
sarcolemma CC 2.5 (0.0352) 17 (27.0) 3.7 (0.0326) 5 (7.9) 2.5 (0.0296) 17 (27.0)
structural constituent of muscle MF 2.7 (0.0487) 13 (29.5) 4.3 (0.0353) 4 (9.1) 2.7 (0.0423) 13 (29.5)
actin binding MF 1.6 (0.0497) 49 (17.5) 2.0 (0.0373) 12 (4.3) 1.6 (0.0404) 49 (17.5)
myeloid cell differentiation BP 4.2 (0.0456) 7 (46.7) 6.3 (0.0434) 2 (13.3) 4.3 (0.0403) 7 (46.7)
sarcomere CC 3.3 (0.00145) 17 (36.2)    3.3 (0.00106) 17 (36.2)
skin morphogenesis BP 9.1 (0.0036) 5 (100.0)    9.2 (0.00292) 5 (100.0)
potassium channel regulator activity MF 3.8 (0.0172) 10 (41.7)    3.8 (0.0141) 10 (41.7)
response to organic cyclic compound BP 2.2 (0.0177) 25 (24.0) 3.2 (0.0274) 7 (6.7)   
response to mechanical stimulus BP 2.8 (0.0383) 13 (31.0) 5.6 (0.0161) 5 (11.9)   
response to glucocorticoid stimulus BP 2.3 (0.0306) 20 (25.3) 3.6 (0.0273) 6 (7.6)   
response to prostaglandin E stimulus BP 6.5 (0.0313) 5 (71.4)    6.6 (0.0277) 5 (71.4)
regulation of muscle contraction BP 5.0 (0.0433) 6 (54.5)    5.0 (0.0383) 6 (54.5)
epidermis development BP 2.2 (0.0448) 19 (24.7) 3.0 (0.0402) 5 (6.5)   
ion transport BP 1.4 (0.0437) 84 (15.7)    1.4 (0.0415) 83 (15.5)
PR of GMSFP' BP 7.3 (0.0493) 4 (80.0)    7.4 (0.0441) 4 (80.0)
troponin complex CC 5.7 (0.0495) 5 (62.5)    5.7 (0.0442) 5 (62.5)
phosphatase binding MF 5.7 (0.0495) 5 (62.5)    5.7 (0.0442) 5 (62.5)
  1. GO categories that are significantly enriched (q < 0.05) during three comparisons are shown. Twelve pathways especially relevant to RA are placed in the top part of the table while other pathways are show at the bottom. Within each section, the number of significant comparisons orders the pathways. If multiple GO categories are significantly enriched in the same number of comparison then an average q values is used for ordering. Only GO categories found as significantly enriched in three or more comparisons are shown. # denotes the number of DMGs in the selected pathway. The GO category 'positive regulation of granulocyte macrophage colony-stimulating factor production' is abbreviated to 'PR of GMSFP' and category 'regulation of fibroblast growth factor receptor signaling pathway' is abbreviated to 'fibroblast growth factor receptor signaling'. The GO types stand for: BP: biological process; CC: cellular component; MF: molecular function.