Table I. PDE vs HPPDB top 100 higher and Top 100 lower ranked significantly enriched specific biological processes.
| Enriched biological processes from proteins in PDE (vs. HPPDB)a | Homo sapiens (20972) | Observed | Expected | Fold enrichment | p-Valueb |
|---|---|---|---|---|---|
| Top 100 higher ranked | |||||
| Supramolecular fiber organization (GO:0097435) | 374 | 12 | 1.78 | 6.73 | 2.16E-03 |
| Tissue development (GO:0009888) | 1643 | 24 | 7.83 | 3.06 | 5.27E-03 |
| Macromolecule catabolic process (GO:0009057) | 962 | 18 | 4.59 | 3.92 | 5.63E-03 |
| Regulation of cellular component organization (GO:0051128) | 2321 | 29 | 11.07 | 2.62 | 6.78E-03 |
| System development (GO:0048731) | 4156 | 41 | 19.82 | 2.07 | 8.56E-03 |
| Protein targeting to membrane (GO:0006612) | 162 | 8 | 0.77 | 10.36 | 1.07E-02 |
| Vesicle-mediated transport (GO:0016192) | 1748 | 24 | 8.33 | 2.88 | 1.58E-02 |
| Regulation of biological quality (GO:0065008) | 3487 | 36 | 16.63 | 2.17 | 1.99E-02 |
| Cellular developmental process (GO:0048869) | 3534 | 36 | 16.85 | 2.14 | 2.74E-02 |
| Symbiosis, encompassing mutualism through parasitism (GO:0044403) | 789 | 15 | 3.76 | 3.99 | 4.44E-02 |
| Organonitrogen compound metabolic process (GO:1901564) | 5458 | 47 | 26.03 | 1.81 | 4.44E-02 |
| Elastic fiber assembly (GO:0048251) | 7 | 3 | 0.03 | 89.88 | 4.98E-02 |
| Regulation of hyaluronan biosynthetic process (GO:1900125) | 7 | 3 | 0.03 | 89.88 | 4.98E-02 |
| Top 100 lower ranked | |||||
| Neutrophil degranulation (GO:0043312) | 483 | 24 | 2.3 | 10.42 | 6.16E-14 |
| Platelet degranulation (GO:0002576) | 127 | 15 | 0.61 | 24.77 | 7.16E-13 |
| Oxidation-reduction process (GO:0055114) | 951 | 19 | 4.53 | 4.19 | 9.64E-04 |
| Killing of cells of other organism (GO:0031640) | 48 | 6 | 0.23 | 26.21 | 1.21E-03 |
| Negative regulation of endopeptidase activity (GO:0010951) | 239 | 10 | 1.14 | 8.77 | 2.14E-03 |
| Monosaccharide biosynthetic process (GO:0046364) | 54 | 6 | 0.26 | 23.3 | 2.40E-03 |
| Antimicrobial humoral response (GO:0019730) | 95 | 7 | 0.45 | 15.45 | 3.68E-03 |
| Response to metal ion (GO:0010038) | 321 | 11 | 1.53 | 7.19 | 3.72E-03 |
| Defence response to fungus (GO:0050832) | 33 | 5 | 0.16 | 31.78 | 5.45E-03 |
| Cellular aldehyde metabolic process (GO:0006081) | 65 | 6 | 0.31 | 19.36 | 6.99E-03 |
| Positive regulation of immune system process (GO:0002684) | 1005 | 18 | 4.79 | 3.76 | 1.05E-02 |
| Blood coagulation (GO:0007596) | 294 | 10 | 1.4 | 7.13 | 1.37E-02 |
| Acute-phase response (GO:0006953) | 40 | 5 | 0.19 | 26.21 | 1.39E-02 |
| Cellular response to tumor necrosis factor (GO:0071356) | 235 | 9 | 1.12 | 8.03 | 1.80E-02 |
| Regulation of cell proliferation (GO:0042127) | 1558 | 22 | 7.43 | 2.96 | 2.98E-02 |
| Ossification (GO:0001503) | 251 | 9 | 1.2 | 7.52 | 3.05E-02 |
| Positive regulation of response to stimulus (GO:0048584) | 2088 | 26 | 9.96 | 2.61 | 3.21E-02 |
| Regulation of generation of precursor metabolites and energy (GO:0043467) | 89 | 6 | 0.42 | 14.14 | 4.20E-02 |
| Aging (GO:0007568) | 262 | 9 | 1.25 | 7.2 | 4.30E-02 |
| Glucose 6-phosphate metabolic process (GO:0051156) | 23 | 4 | 0.11 | 36.47 | 4.43E-02 |
| Organonitrogen compound metabolic process (GO:1901564) | 5458 | 47 | 26.03 | 1.81 | 4.44E-02 |
amost specific significantly enriched biological processes from Gene Ontology (full hierarchical list is given in supplemental Table S7).
bBonferroni corrected for multiple testing.