Table 5 The top 15 significant changes in GO-BP (A), −CC (B), −MF(C) and KEGG pathway (D) according to differentially expressed genes in MALAT1-ceRNA sub-network

 GO-BP Term

Enrichment Score

Count

%

P-Value

 positive regulation of transcription from RNA polymerase II promoter

3.579259

20

11.43

<  0.001

 transcription from RNA polymerase II promoter

3.106442

13

7.429

<  0.001

positive regulation of transcription, DNA-templated

3.091753

13

7.429

<  0.001

 neuroepithelial cell differentiation

2.894845

3

1.714

0.001

 positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway

2.772993

4

2.286

0.002

 neural tube formation

2.772164

3

1.714

0.002

 in utero embryonic development

2.425229

7

4

0.004

 kidney development

2.315189

5

2.857

0.005

 camera-type eye morphogenesis

2.158154

3

1.714

0.007

 regulation of protein localization

2.092037

4

2.286

0.008

 inner ear morphogenesis

2.092037

4

2.286

0.008

 positive regulation of branching involved in ureteric bud morphogenesis

2.011071

3

1.714

0.01

 positive regulation of neuroblast proliferation

1.967555

3

1.714

0.011

 negative regulation of transcription from RNA  polymerase II promoter

1.923719

13

7.429

0.012

 cell migration

1.922663

6

3.429

0.012

 GO-CC Term

Enrichment Score

Count

%

P-Value

 cytosol

3.530641

45

25.71

<  0.001

 nucleus

3.429028

64

36.57

<  0.001

 nucleoplasm

3.288165

39

22.29

<  0.001

 cell-cell adherens junction

2.341584

9

5.143

0.005

 melanosome

2.052614

5

2.857

0.009

 filopodium

1.71293

4

2.286

0.019

 PcG protein complex

1.707154

3

1.714

0.02

 nuclear chromatin

1.705842

6

3.429

0.02

 extracellular exosome

1.429256

32

18.29

0.037

 cis-Golgi network

1.35117

3

1.714

0.045

 spindle microtubule

1.314751

3

1.714

0.048

 cytoplasm

1.239444

52

29.71

0.058

 perinuclear region of cytoplasm

1.205186

10

5.714

0.062

 membrane

1.146558

25

14.29

0.071

 spindle

1.134303

4

2.286

0.073

 GO-MF Term

Enrichment Score

Count

%

P-Value

 protein binding

3.880727

95

54.29

<  0.001

 sequence-specific DNA binding

3.451663

14

8

<  0.001

 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding

3.120112

9

5.143

<  0.001

 RNA polymerase II core promoter proximal region sequence-specific DNA binding

2.566023

10

5.714

0.003

 poly(A) RNA binding

2.27862

19

10.86

0.005

 transcription factor activity, sequence-specific DNA binding

1.893028

16

9.143

0.013

 zinc ion binding

1.508313

17

9.714

0.031

 cadherin binding involved in cell-cell adhesion

1.481723

7

4

0.033

 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding

1.359345

4

2.286

0.044

 vascular endothelial growth factor receptor 2 binding

1.315103

2

1.143

0.048

 N6-methyladenosine-containing RNA binding

1.249923

2

1.143

0.056

 mRNA 5′-UTR binding

1.144306

2

1.143

0.072

 protein heterodimerization activity

1.046398

8

4.571

0.09

 RNA polymerase II regulatory region sequence-specific DNA binding

1.031152

5

2.857

0.093

 DNA binding

1.029587

20

11.43

0.093

 GO-MF Term

Enrichment Score

Count

%

P-Value

 protein binding

3.880727

95

54.29

<  0.001

 sequence-specific DNA binding

3.451663

14

8

<  0.001

 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding

3.120112

9

5.143

<  0.001

 RNA polymerase II core promoter proximal region sequence-specific DNA binding

2.566023

10

5.714

0.003

 poly(A) RNA binding

2.27862

19

10.86

0.005

 transcription factor activity, sequence-specific DNA binding

1.893028

16

9.143

0.013

 zinc ion binding

1.508313

17

9.714

0.031

 cadherin binding involved in cell-cell adhesion

1.481723

7

4

0.033

 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding

1.359345

4

2.286

0.044

 vascular endothelial growth factor receptor 2 binding

1.315103

2

1.143

0.048

 N6-methyladenosine-containing RNA binding

1.249923

2

1.143

0.056

 mRNA 5′-UTR binding

1.144306

2

1.143

0.072

 protein heterodimerization activity

1.046398

8

4.571

0.09

RNA polymerase II regulatory region sequence-specific DNA binding

1.031152

5

2.857

0.093

 DNA binding

1.029587

20

11.43

0.093