Table 2 Modules for the PRAD dataset ranked by percentage of functionally enigmatic genes.

From: Functionally Enigmatic Genes in Cancer: Using TCGA Data to Map the Limitations of Annotations

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
  1. 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.