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Table 3 Top 5 clusters of Gene Ontology terms enriched in the 2,405 optimal ceRNAs

From: Parameter optimization for constructing competing endogenous RNA regulatory network in glioblastoma multiforme and other cancers

GO Term No. of genes Bonferroni adjusted P-value Total No. of optimal ceRNA pairs/ceRNAs GBM corea OV corea LUSC corea LAML corea CV among cancersb
Cluster 1 (Enrichment Score: 17.99)
GO:0046907~intracellular transport 184 9.26E-18       
GO:0008104~protein localization 225 7.88E-17       
GO:0015031~protein transport 200 4.67E-16       
GO:0045184~establishment of protein localization 201 6.18E-16 8229/261 7152/261 6235/258 3961/254 2755/247 34.85%/2.06%
GO:0070727~cellular macromolecule localization 126 2.75E-14       
GO:0034613~cellular protein localization 124 1.09E-13       
GO:0006886~intracellular protein transport 111 3.17E-11       
Cluster 2 (Enrichment Score: 8.27)
GO:0009057~macromolecule catabolic process 180 2.95E-08       
GO:0044265~cellular macromolecule catabolic process 168 1.04E-07       
GO:0030163~protein catabolic process 143 6.75E-06       
GO:0043632~modification-dependent macromolecule catabolic process 134 8.41E-06       
GO:0019941~modification-dependent protein catabolic process 134 8.41E-06 4838/200 4418/200 3836/197 2379/193 2049/191 31.08%/1.79%
GO:0051603~proteolysis involved in cellular protein catabolic process 138 1.31E-05       
GO:0044257~cellular protein catabolic process 138 1.85E-05       
GO:0006511~ubiquitin-dependent protein catabolic process 68 8.96E-05       
GO:0006508~proteolysis 177 1       
Cluster 3 (Enrichment Score: 6.01)
GO:0016192~vesicle-mediated transport 141 8.98E-08       
GO:0016044~membraneorganization 93 3.70E-04 3462/157 2882/155 2519/156 1607/149 1208/147 32.82%/2.53%
GO:0010324~membrane invagination 50 0.935246       
GO:0006897~endocytosis 50 0.935246       
Cluster 4 (Enrichment Score: 5.67)
GO:0032446~protein modification by small protein conjugation 45 6.85E-05       
GO:0070647~protein modification by small protein conjugation or removal 50 2.36E-04       
GO:0016567~protein ubiquitination 40 7.30E-04       
GO:0019787~small conjugating protein ligase activity 45 0.012039 607/67 555/67 488/66 335/65 266/62 28.13%/2.88%
GO:0016881~acid-amino acid ligase activity 51 0.020482       
GO:0004842~ubiquitin-protein ligase activity 39 0.084550       
GO:0016879~ligase activity, forming carbon-nitrogen bonds 53 0.213866       
Cluster 5 (Enrichment Score: 5.10)
GO:0010608~posttranscription al regulation of gene expression 59 0.001017       
GO:0006417~regulation of translation 40 0.036298 1312/105 1132/105 961/101 643/99 480/100 31.90%/2.25%
GO:0032268~regulation of cellular protein metabolic process 96 0.576893       
  1. a Number of optimal ceRNA pairs/ceRNAs with significant positive correlation coefficients in corresponding cancer dataset, b Coefficients of variation of number of core ceRNA pairs/ceRNAs among four cancer datasets.