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 | Â | Combined | OA+NL | OA or NL | |||
|---|---|---|---|---|---|---|---|
Comparison description | Â | 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) | Â | Â | 3.3 (0.0141) | 12 (36.4) |
cell adhesion | BP | 1.4 (0.0425) | 84 (15.7) | Â | Â | 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) | Â | Â | 3.3 (0.00106) | 17 (36.2) |
skin morphogenesis | BP | 9.1 (0.0036) | 5 (100.0) | Â | Â | 9.2 (0.00292) | 5 (100.0) |
potassium channel regulator activity | MF | 3.8 (0.0172) | 10 (41.7) | Â | Â | 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) | Â | Â |
response to mechanical stimulus | BP | 2.8 (0.0383) | 13 (31.0) | 5.6 (0.0161) | 5 (11.9) | Â | Â |
response to glucocorticoid stimulus | BP | 2.3 (0.0306) | 20 (25.3) | 3.6 (0.0273) | 6 (7.6) | Â | Â |
response to prostaglandin E stimulus | BP | 6.5 (0.0313) | 5 (71.4) | Â | Â | 6.6 (0.0277) | 5 (71.4) |
regulation of muscle contraction | BP | 5.0 (0.0433) | 6 (54.5) | Â | Â | 5.0 (0.0383) | 6 (54.5) |
epidermis development | BP | 2.2 (0.0448) | 19 (24.7) | 3.0 (0.0402) | 5 (6.5) | Â | Â |
ion transport | BP | 1.4 (0.0437) | 84 (15.7) | Â | Â | 1.4 (0.0415) | 83 (15.5) |
PR of GMSFP' | BP | 7.3 (0.0493) | 4 (80.0) | Â | Â | 7.4 (0.0441) | 4 (80.0) |
troponin complex | CC | 5.7 (0.0495) | 5 (62.5) | Â | Â | 5.7 (0.0442) | 5 (62.5) |
phosphatase binding | MF | 5.7 (0.0495) | 5 (62.5) | Â | Â | 5.7 (0.0442) | 5 (62.5) |