Table 1

Gene Ontology enrichment analysis
Rank BIOLOGICAL PROCESS GO ID Reference Genes Observed Genes Ratio
1 regulation of lymphocyte proliferation GO:0050670 81 32 39.51%
2 regulation of leukocyte proliferation GO:0070663 82 32 39.02%
3 regulation of mononuclear cell proliferation GO:0032944 82 32 39.02%
4 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains GO:0002460 112 38 33.93%
5 adaptive immune response GO:0002250 113 38 33.63%
6 lymphocyte proliferation GO:0046651 112 37 33.04%
7 leukocyte proliferation GO:0070661 114 37 32.46%
8 mononuclear cell proliferation GO:0032943 114 37 32.46%
9 regulation of lymphocyte activation GO:0051249 141 42 29.79%
10 regulation of cell activation GO:0050865 168 46 27.38%
11 regulation of leukocyte activation GO:0002694 159 43 27.04%
12 positive regulation of immune system process GO:0002684 229 60 26.20%
13 regulation of immune response GO:0050776 218 54 24.77%
14 immune effector process GO:0002252 200 45 22.50%
15 regulation of immune system process GO:0002682 362 79 21.82%
16 lymphocyte activation GO:0046649 272 59 21.69%
17 leukocyte activation GO:0045321 324 66 20.37%
18 inflammatory response GO:0006954 359 71 19.78%
19 cell activation GO:0001775 366 71 19.40%
20 immune response GO:0006955 750 133 17.73%
21 regulation of response to stimulus GO:0048583 441 75 17.01%
22 defense response GO:0006952 657 100 15.22%
23 immune system process GO:0002376 1066 162 15.20%
24 response to wounding GO:0009611 560 85 15.18%
25 response to external stimulus GO:0009605 904 110 12.17%
26 multi-organism process GO:0051704 668 79 11.83%
27 regulation of programmed cell death GO:0043067 812 92 11.33%
28 regulation of apoptosis GO:0042981 805 91 11.30%
29 regulation of cell death GO:0010941 815 92 11.29%
30 regulation of cell proliferation GO:0042127 739 79 10.69%
31 apoptosis GO:0006915 1063 102 9.60%
32 programmed cell death GO:0012501 1071 102 9.52%
33 response to chemical stimulus GO:0042221 1243 117 9.41%
34 cell proliferation GO:0008283 1056 98 9.28%
35 death GO:0016265 1171 107 9.14%
36 cell death GO:0008219 1167 106 9.08%
37 response to stress GO:0006950 1696 144 8.49%
38 positive regulation of biological process GO:0048518 1865 153 8.20%
39 positive regulation of cellular process GO:0048522 1699 130 7.65%
40 response to stimulus GO:0050896 3471 221 6.37%
Rank CELLULAR COMPONENT GO ID Count Observed Ratio
1 calcineurin complex GO:0005955 5 3 60.00%
2 external side of plasma membrane GO:0009897 131 40 30.53%
3 platelet alpha granule lumen GO:0031093 41 12 29.27%
4 MHC class II protein complex GO:0042613 14 4 28.57%
5 nerve terminal GO:0043679 14 4 28.57%
6 cytoplasmic membrane-bounded vesicle lumen GO:0060205 44 12 27.27%
7 vesicle lumen GO:0031983 46 12 26.09%
8 integrin complex GO:0008305 29 7 24.14%
9 platelet alpha granule GO:0031091 52 12 23.08%
10 high-density lipoprotein particle GO:0034364 24 5 20.83%
11 MHC protein complex GO:0042611 38 7 18.42%
12 plasma lipoprotein particle GO:0034358 34 6 17.65%
13 protein-lipid complex GO:0032994 34 6 17.65%
14 cell surface GO:0009986 305 51 16.72%
15 axon part GO:0033267 48 7 14.58%
16 extracellular space GO:0005615 670 84 12.54%
17 receptor complex GO:0043235 113 13 11.50%
18 secretory granule GO:0030141 174 19 10.92%
19 membrane raft GO:0045121 131 14 10.69%
20 extracellular region part GO:0044421 939 94 10.01%
21 axon GO:0030424 148 14 9.46%
22 cell soma GO:0043025 155 13 8.39%
23 soluble fraction GO:0005625 297 24 8.08%
24 cytoplasmic vesicle part GO:0044433 177 13 7.34%
25 extracellular region GO:0005576 1984 143 7.21%
26 basolateral plasma membrane GO:0016323 190 13 6.84%
27 lysosome GO:0005764 206 14 6.80%
28 integral to plasma membrane GO:0005887 1183 72 6.09%
29 intrinsic to plasma membrane GO:0031226 1206 73 6.05%
30 cytoplasmic membrane-bounded vesicle GO:0016023 537 32 5.96%
31 membrane-bounded vesicle GO:0031988 555 32 5.77%
32 extracellular matrix GO:0031012 335 19 5.67%
33 neuron projection GO:0043005 318 18 5.66%
34 plasma membrane part GO:0044459 1918 104 5.42%
35 cell fraction GO:0000267 1039 55 5.29%
36 cytoplasmic vesicle GO:0031410 628 33 5.25%
37 vesicle GO:0031982 655 33 5.04%
38 insoluble fraction GO:0005626 803 34 4.23%
39 plasma membrane GO:0005886 3650 139 3.81%
40 cytosol GO:0005829 1251 47 3.76%
Rank MOLECULAR FUNCTION GO ID COUNT Observed RATIO
1 arginine binding GO:0034618 3 3 100.00%
2 nitric-oxide synthase activity GO:0004517 3 3 100.00%
3 tetrahydrobiopterin binding GO:0034617 3 3 100.00%
4 C-X-C chemokine binding GO:0019958 8 4 50.00%
5 beta-amyloid binding GO:0001540 13 5 38.46%
6 tumor necrosis factor receptor binding GO:0005164 21 8 38.10%
7 chemokine activity GO:0008009 47 17 36.17%
8 chemokine receptor binding GO:0042379 49 17 34.69%
9 coreceptor activity GO:0015026 19 6 31.58%
10 tumor necrosis factor receptor superfamily binding GO:0032813 31 9 29.03%
11 cytokine receptor binding GO:0005126 178 46 25.84%
12 chemokine binding GO:0019956 26 6 23.08%
13 cytokine activity GO:0005125 196 45 22.96%
14 growth factor receptor binding GO:0070851 67 14 20.90%
15 collagen binding GO:0005518 35 7 20.00%
16 G-protein-coupled receptor binding GO:0001664 107 20 18.69%
17 integrin binding GO:0005178 58 9 15.52%
18 cysteine-type endopeptidase activity GO:0004197 71 10 14.08%
19 growth factor activity GO:0008083 161 19 11.80%
20 cytokine binding GO:0019955 108 12 11.11%
21 protein heterodimerization activity GO:0046982 189 21 11.11%
22 glycosaminoglycan binding GO:0005539 139 14 10.07%
23 protein complex binding GO:0032403 196 19 9.69%
24 receptor binding GO:0005102 856 83 9.70%
25 receptor signaling protein activity GO:0005057 159 15 9.43%
26 pattern binding GO:0001871 153 14 9.15%
27 peptidase inhibitor activity GO:0030414 154 14 9.09%
28 carbohydrate binding GO:0030246 349 29 8.31%
29 endopeptidase activity GO:0004175 370 28 7.57%
30 polysaccharide binding GO:0030247 153 14 9.15%
31 protein dimerization activity GO:0046983 514 36 7.00%
32 identical protein binding GO:0042802 618 38 6.15%
33 enzyme binding GO:0019899 505 29 5.74%
34 peptidase activity GO:0008233 563 30 5.33%
35 peptidase activity, acting on L-amino acid peptides GO:0070011 546 29 5.31%
36 molecular transducer activity GO:0060089 2116 98 4.63%
37 signal transducer activity GO:0004871 2116 98 4.63%
38 receptor activity GO:0004872 1674 71 4.24%
39 protein binding GO:0005515 8041 280 3.48%
40 binding GO:0005488 12465 320 2.57%

The table ranks the gene enrichment in biological processes, cellular component and molecular function with corresponding GO IDs. For each GO ID, the number of Observed Genes identified in the SSKB was divided by the number of Reference Genes in the human genome to calculate the Ratio of enrichment (Ratio).

Gorr et al.

Gorr et al. BMC Musculoskeletal Disorders 2012 13:119   doi:10.1186/1471-2474-13-119

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