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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]