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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.