Table 2.
Modules for the PRAD dataset ranked by percentage of functionally enigmatic genes.
| PRAD Module Color | Total Genes | Functionally Enigmatic (%) | Unmapped in STRING (%) | PPI Enrichment p-value | GO Biological Process Term Description | ||
|---|---|---|---|---|---|---|---|
| green | 336 | 80.95 | 8 | <1.00E-16 | mRNA processing | mRNA splice site selection | spliceosomal complex assembly |
| cyan | 60 | 80 | 4 | 6.35E-06 | translational initiation | mRNA export from nucleus | mRNA-containing ribonucleoprotein complex export from nucleus |
| magenta | 137 | 77.37 | 6 | <1.00E-16 | RNA splicing | mRNA processing | RNA processing |
| turquoise | 3163 | 74.01 | 1 | <1.00E-16 | intracellular transport | single-organism intracellular transport | establishment of protein localization |
| yellow | 823 | 71.81 | 1 | <1.00E-16 | single-organism intracellular transport | intracellular transport | neurogenesis |
| brown | 974 | 70.12 | 1 | <1.00E-16 | chromatin modification | chromosome organization | peptidyl-lysine modification |
| salmon | 72 | 69.45 | 4 | 4.28E-10 | positive regulation of cellular protein metabolic process | inositol biosynthetic process | Golgi reassembly |
| blue | 1451 | 67.26 | 1 | <1.00E-16 | cell morphogenesis involved in differentiation | extracellular matrix organization | extracellular structure organization |
| lightcyan | 40 | 65 | 4 | 5.25E-14 | muscle structure development | muscle filament sliding | actin-myosin filament sliding |
| grey60 | 40 | 62.5 | 2 | <1.00E-16 | defense response to virus | response to virus | type I interferon signaling pathway |
| red | 285 | 62.11 | 0 | 1.75E-12 | response to hormone | response to oxygen-containing compound | organonitrogen compound metabolic process |
| black | 269 | 60.45 | 1 | <1.00E-16 | tissue development | epithelium development | cell adhesion |
| midnightblue | 57 | 50.87 | 3 | <1.00E-16 | vasculature development | blood vessel development | angiogenesis |
| purple | 127 | 50.39 | 1% | <1.00E-16 | extracellular matrix organization | extracellular structure organization | collagen metabolic process |
| pink | 234 | 43.59 | 2 | <1.00E-16 | immune response | defense response | positive regulation of immune system process |
| greenyellow | 103 | 40.73 | 2% | <1.00E-16 | response to organic cyclic compound | response to lipid | negative regulation of gene expression |
| tan | 90 | 34.44 | 1% | <1.00E-16 | cell cycle | mitotic cell cycle | cell cycle process |
All modules were enriched for known protein-protein interactions within the STRING database, indicating that genes known to interact were grouped together. Top three GO Biological Process are shown; italics indicates enrichment for term was not significant at an FDR-corrected value of <0.05; all others were statistically significant. Full statistics are shown in Supplementary Table 2 along with other data sets.