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Table 4 Enrichment analysis for each comparison across all ‘omics types, with q-values, and the literature references mentioning involvement of the terms in ovarian cancer development. Q-values are the minimal false discovery rate at which the test may be called significant, or in other words, the p-value threshold to satisfy the FDR criteria set by the Benjamini-Hochberg procedure

From: A computational framework for complex disease stratification from multiple large-scale datasets

Term

Term type

‘Omic type

Contrast

q-value

Reference of implication in ovarian cancer

E2F

Transcription factor

Transcriptomics

1 vs Rest

8.17E-48

[123, 124]

Sp1

Transcription factor

Transcriptomics

1 vs Rest

1.95E-35

[125]

Mitochondrial translation

Reactome

Transcriptomics

1 vs Rest

9.02E-21

[126]

hsa-miR-193a-5p

miRNA

Transcriptomics

1 vs Rest

4.33E-09

[127]

CREM

Transcription factor

Methylation

1 vs Rest

2.45E-03

[128]

hsa-miR-940

miRNA

Transcriptomics

1 vs Rest

6.80E-03

[129]

hsa-miR-601

miRNA

Transcriptomics

1 vs Rest

6.81E-03

[129]

hsa-miR-503

miRNA

Transcriptomics

1 vs Rest

1.41E-02

[129]

AP-1

Transcription factor

Methylation

1 vs Rest

1.52E-02

[130]

TCF-4

Transcription factor

Methylation

1 vs Rest

2.04E-02

[131]

hsa-miR-361-3p

miRNA

Transcriptomics

1 vs Rest

2.53E-02

[129]

C/EBP

Transcription factor

Methylation

2 vs Rest

1.13E-05

[132]

LMXB1

Transcription factor

Methylation

2 vs Rest

9.32E-05

[133]

hsa-miR-330-5p

miRNA

Transcriptomics

2 vs Rest

7.57E-03

[134]

Chemical carcinogenesis

KEGG pathways

Transcriptomics

2 vs Rest

1.77E-02

[135,136,137]

hsa-miR-335

miRNA

Transcriptomics

2 vs Rest

3.95E-02

[138]

MZF-1

Transcription factor

Transcriptomics

3 vs Rest

4.06E-39

[139]

SREBP-1

Transcription factor

Transcriptomics

3 vs Rest

5.29E-38

[140]

AP-2gamma

Transcription factor

Transcriptomics

3 vs Rest

1.79E-36

[141]

GPCR ligand binding

Reactome

Transcriptomics

3 vs Rest

8.14E-10

[142]

hsa-miR-328

miRNA

Transcriptomics

3 vs Rest

9.92E-10

[129]

hsa-miR-370

miRNA

Transcriptomics

3 vs Rest

1.09E-08

[129]

hsa-miR-601

miRNA

Transcriptomics

3 vs Rest

1.07E-07

[129]

hsa-miR-423-5p

miRNA

Transcriptomics

3 vs Rest

1.36E-06

[129]

hsa-miR-139-3p

miRNA

Transcriptomics

3 vs Rest

2.28E-05

[129]

hsa-miR-769-5p

miRNA

Transcriptomics

3 vs Rest

9.05E-05

[129]

hsa-miR-339-3p

miRNA

Transcriptomics

3 vs Rest

2.16E-04

[129]

hsa-miR-940

miRNA

Transcriptomics

3 vs Rest

2.94E-04

[129]

hsa-miR-542-5p

miRNA

Transcriptomics

3 vs Rest

8.13E-04

[129]

hsa-miR-483-5p

miRNA

Transcriptomics

3 vs Rest

1.50E-03

[129]

hsa-miR-361-3p

miRNA

Transcriptomics

3 vs Rest

7.88E-03

[129]

hsa-miR-449a

miRNA

Transcriptomics

3 vs Rest

4.87E-02

[129]

T cell aggregation

GO Biological Process

Transcriptomics

4 vs Rest

1.94E-38

[143]

T cell activation

GO Biological Process

Transcriptomics

4 vs Rest

1.94E-38

[144]

Natural killer cell mediated cytotoxicity

KEGG pathways

Transcriptomics

4 vs Rest

8.60E-14

[145]

Cell adhesion molecules (CAMs)

KEGG pathways

Transcriptomics

4 vs Rest

2.37E-11

[146]

Hedgehog ‘on’ state

Reactome

Transcriptomics

4 vs Rest

7.21E-05

[147]

HIC1

Transcription factor

Methylation

4 vs Rest

2.46E-04

[148]

hsa-miR-328

miRNA

Transcriptomics

4 vs Rest

1.49E-02

[129]

AP-2gamma

Transcription factor

Transcriptomics

4 vs Rest

3.00E-02

[141]

T cell activation

GO Biological Process

Transcriptomics

5 vs Rest

1.94E-38

[144]

T cell aggregation

GO Biological Process

Transcriptomics

5 vs Rest

2.25E-22

[143]

Natural killer cell mediated cytotoxicity

KEGG pathways

Transcriptomics

5 vs Rest

8.60E-14

[145]

Antigen processing and presentation

KEGG pathways

Transcriptomics

5 vs Rest

4.33E-11

[149]

Interferon alpha/beta signalling

Reactome

Transcriptomics

5 vs Rest

6.11E-08

[150]

hsa-miR-423-5p

miRNA

Transcriptomics

5 vs Rest

3.09E-05

[129]

hsa-miR-328

miRNA

Transcriptomics

5 vs Rest

5.23E-04

[129]

VEGFA-VEGFR2 Pathway

Reactome

Transcriptomics

5 vs Rest

2.57E-03

[151, 152]

Hedgehog ‘off’ state

Reactome

Transcriptomics

5 vs Rest

1.21E-02

[153]

hsa-miR-139-3p

miRNA

Transcriptomics

5 vs Rest

1.35E-02

[129]

NF- κB signalling pathway

KEGG pathways

Transcriptomics

5 vs Rest

1.53E-02

[154]

hsa-miR-601

miRNA

Transcriptomics

5 vs Rest

2.71E-02

[129]

Jak-STAT signalling pathway

KEGG pathways

Transcriptomics

5 vs Rest

3.54E-02

[155]

hsa-miR-375

miRNA

Transcriptomics

5 vs Rest

3.74E-02

[129]

Signalling by GPCR

Reactome

Transcriptomics

6 vs Rest

1.24E-14

[156]

hsa-miR-328

miRNA

Transcriptomics

6 vs Rest

1.47E-08

[129]

hsa-miR-601

miRNA

Transcriptomics

6 vs Rest

6.94E-07

[129]

hsa-miR-370

miRNA

Transcriptomics

6 vs Rest

2.46E-06

[129]

hsa-miR-423-5p

miRNA

Transcriptomics

6 vs Rest

4.81E-06

[129]

hsa-miR-423-3p

miRNA

Transcriptomics

6 vs Rest

1.77E-05

[129]

cAMP metabolic process

GO Biological Process

Transcriptomics

6 vs Rest

9.22E-05

[157]

hsa-miR-769-5p

miRNA

Transcriptomics

6 vs Rest

5.13E-04

[129]

hsa-miR-139-3p

miRNA

Transcriptomics

6 vs Rest

2.70E-03

[129]

hsa-miR-483-5p

miRNA

Transcriptomics

6 vs Rest

4.90E-03

[129]

hsa-miR-940

miRNA

Transcriptomics

6 vs Rest

5.05E-03

[129]

T cell selection

GO Biological Process

Transcriptomics

6 vs Rest

1.41E-02

[158]

Arachidonic acid metabolism

KEGG pathways

Transcriptomics

6 vs Rest

1.42E-02

[135]

hsa-miR-542-5p

miRNA

Transcriptomics

6 vs Rest

1.73E-02

[129]

Oxidative phosphorylation

KEGG pathways

Transcriptomics

7 vs Rest

9.49E-13

[159]

Stabilization of p53

Reactome

Transcriptomics

7 vs Rest

1.06E-07

[160]

Spliceosome

KEGG pathways

Transcriptomics

7 vs Rest

1.59E-07

[161]

NF-kB signalling pathway

Reactome

Transcriptomics

7 vs Rest

3.97E-05

[154]

hsa-miR-542-5p

miRNA

Transcriptomics

7 vs Rest

2.53E-03

[129]

hsa-miR-601

miRNA

Transcriptomics

7 vs Rest

2.62E-03

[129]

hsa-miR-423-5p

miRNA

Transcriptomics

7 vs Rest

5.88E-03

[129]

hsa-let-7c

miRNA

Transcriptomics

7 vs Rest

2.67E-02

[129]

Regulation of HIF by oxygen

Reactome

Transcriptomics

7 vs Rest

3.32E-02

[162]

hsa-miR-361-3p

miRNA

Transcriptomics

7 vs Rest

4.16E-02

[129]

hsa-miR-328

miRNA

Transcriptomics

8 vs Rest

9.25E-15

[129]

hsa-miR-370

miRNA

Transcriptomics

8 vs Rest

3.60E-11

[129]

hsa-miR-940

miRNA

Transcriptomics

8 vs Rest

1.37E-10

[129]

hsa-miR-423-5p

miRNA

Transcriptomics

8 vs Rest

4.29E-10

[129]

hsa-miR-423-3p

miRNA

Transcriptomics

8 vs Rest

7.47E-09

[129]

hsa-miR-139-3p

miRNA

Transcriptomics

8 vs Rest

5.08E-07

[129]

hsa-miR-601

miRNA

Transcriptomics

8 vs Rest

9.47E-07

[129]

hsa-miR-542-5p

miRNA

Transcriptomics

8 vs Rest

4.72E-04

[129]

hsa-miR-361-3p

miRNA

Transcriptomics

8 vs Rest

1.07E-03

[129]

hsa-miR-483-5p

miRNA

Transcriptomics

8 vs Rest

1.32E-03

[129]

hsa-miR-769-5p

miRNA

Transcriptomics

8 vs Rest

1.68E-03

[129]

Potassium signalling pathway

Reactome

Transcriptomics

8 vs Rest

1.15E-02

[163]

hsa-miR-99b

miRNA

Transcriptomics

8 vs Rest

1.93E-02

[129]

hsa-miR-339-3p

miRNA

Transcriptomics

8 vs Rest

2.28E-02

[129]

T cell lineage commitment

GO Biological Process

Transcriptomics

8 vs Rest

3.80E-02

[164]

hsa-miR-139-3p

miRNA

Transcriptomics

9 vs Rest

3.58E-09

[129]

hsa-miR-423-5p

miRNA

Transcriptomics

9 vs Rest

5.89E-09

[129]

hsa-miR-328

miRNA

Transcriptomics

9 vs Rest

2.32E-08

[129]

hsa-miR-370

miRNA

Transcriptomics

9 vs Rest

4.83E-08

[129]

hsa-miR-423-3p

miRNA

Transcriptomics

9 vs Rest

3.89E-06

[129]

hsa-miR-940

miRNA

Transcriptomics

9 vs Rest

5.37E-06

[129]

hsa-miR-769-5p

miRNA

Transcriptomics

9 vs Rest

1.07E-04

[129]

hsa-miR-339-3p

miRNA

Transcriptomics

9 vs Rest

0.000173

[129]

hsa-miR-601

miRNA

Transcriptomics

9 vs Rest

2.05E-04

[129]

hsa-miR-483-5p

miRNA

Transcriptomics

9 vs Rest

7.33E-03

[129]

Calcium signalling pathway

KEGG pathways

Transcriptomics

9 vs Rest

1.55E-02

[165]

hsa-miR-542-5p

miRNA

Transcriptomics

9 vs Rest

1.69E-02

[129]

cAMP signalling pathway

KEGG pathways

Transcriptomics

9 vs Rest

2.33E-02

[166]

Ion transfer

GO Biological Process

Transcriptomics

9 vs Rest

3.43E-02

[167]

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BMC Systems Biology

ISSN: 1752-0509

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