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Table 6 The top significant changes in GO-BP (A), −CC (B), −MF(C) and KEGG pathway (D) according to differentially expressed genes in LINC00943-ceRNA sub-network

From: Reconstruction of lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveals functional lncRNAs in skin cutaneous melanoma

A

 GO-BP Term

Enrichment Score

Count

%

P-Value

 positive regulation of transcription from RNA polymerase II promoter

3.413985

22

12.22

<  0.001

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

2.5522952

4

2.222

0.003

 negative regulation of transcription from RNA polymerase II promoter

2.4555568

16

8.889

0.004

 transcription from RNA polymerase II promoter

2.4471842

13

7.222

0.004

 positive regulation of transcription, DNA-templated

2.4336944

13

7.222

0.004

 apoptotic process

2.1092412

13

7.222

0.008

 negative regulation of translational initiation

2.064083

3

1.667

0.009

 protein import into mitochondrial matrix

1.95711

3

1.667

0.011

 regulation of protein localization

1.8821494

4

2.222

0.013

 response to cytokine

1.8821494

4

2.222

0.013

 cellular response to cytokine stimulus

1.7404426

3

1.667

0.018

 cell morphogenesis

1.6784701

4

2.222

0.021

 positive regulation of mesenchymal cell proliferation

1.6028585

3

1.667

0.025

 intracellular protein transport

1.6019839

7

3.889

0.025

 protein sumoylation

1.5991972

5

2.778

0.025

B

 GO-CC Term

Enrichment Score

Count

%

P-Value

 cytosol

4.721026

54

30

<  0.001

 nucleoplasm

3.468485

44

24.44

<  0.001

 nucleus

3.459493

72

40

<  0.001

 cytoplasm

3.448156

70

38.89

<  0.001

 membrane

2.786622

35

19.44

0.002

 microtubule plus-end

1.979181

3

1.667

0.01

 PcG protein complex

1.593489

3

1.667

0.025

 nuclear chromatin

1.476598

6

3.333

0.033

 intracellular ribonucleoprotein complex

1.428852

5

2.778

0.037

 mitochondrial outer membrane

1.3075

5

2.778

0.049

 endoplasmic reticulum membrane

1.253057

14

7.778

0.056

 perinuclear region of cytoplasm

1.207393

11

6.111

0.062

 MLL5-L complex

1.146143

2

1.111

0.071

 mitochondrial inner membrane presequence translocase complex

1.096965

2

1.111

0.08

C

 GO-MF Term

Enrichment Score

Count

%

P-Value

 protein binding

3.972219

109

60.56

<  0.001

 protein channel activity

3.7469

4

2.222

<  0.001

 sequence-specific DNA binding

3.320627

15

8.333

<  0.001

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

2.640286

11

6.111

0.002

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

2.106865

8

4.444

0.008

 transcription factor activity, sequence-specific DNA binding

1.648871

17

9.444

0.022

 protein kinase activity

1.643895

9

5

0.023

 ATP binding

1.307149

22

12.22

0.049

 vascular endothelial growth factor receptor 2 binding

1.25008

2

1.111

0.056

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

1.197916

4

2.222

0.063

 N6-methyladenosine-containing RNA binding

1.185193

2

1.111

0.065

 P-P-bond-hydrolysis-driven protein transmembrane transporter activity

1.129258

2

1.111

0.074

 poly(A) RNA binding

1.119963

17

9.444

0.076

 chromatin binding

1.08038

8

4.444

0.083

 mRNA 5′-UTR binding

1.080159

2

1.111

0.083

D

 KEGG pathway

Enrichment Score

Count

%

P-Value

 Pathways in cancer

2.26453

11

6.111

0.005

 PI3K-Akt signaling pathway

2.145933

10

5.556

0.007

 Oocyte meiosis

1.604046

5

2.778

0.025

 Pancreatic cancer

1.566902

4

2.222

0.027

 Platelet activation

1.386975

5

2.778

0.041

 Insulin signaling pathway

1.307592

5

2.778

0.049

 Proteoglycans in cancer

1.304184

6

3.333

0.05

 Focal adhesion

1.259046

6

3.333

0.055

 Rap1 signaling pathway

1.229991

6

3.333

0.059

 Hippo signaling pathway

1.190921

5

2.778

0.064

 MicroRNAs in cancer

1.179653

7

3.889

0.066

 HIF-1 signaling pathway

1.146419

4

2.222

0.071

 Vibrio cholerae infection

1.020041

3

1.667

0.095