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Table 1 Top-k pathways ranked by the iDRW method in breast cancer (k = 25) and neuroblastoma data (k = 5). For each pathway, total number of genes, significant genes from gene expression (EXP) and copy number data (CNA) are shown (p-value of t-test / DESeq2 or χ2-test < 0.05)

From: Robust pathway-based multi-omics data integration using directed random walks for survival prediction in multiple cancer studies

Dataset

Pathway ID

Pathway name

Total genes

EXP

CNA

Breast cancer

hsa04740

Olfactory transduction

419

54

268

hsa04014

Ras signaling pathway

232

68

164

hsa04015

Rap1 signaling pathway

206

64

142

hsa04916

Melanogenesis

101

37

73

hsa04722

Neurotrophin signaling pathway

119

38

84

hsa05200

Pathways in cancer

526

166

359

hsa04933

AGE-RAGE signaling pathway in diabetic complications

99

37

67

hsa04530

Tight junction

170

53

107

hsa04510

Focal adhesion

199

76

125

hsa04080

Neuroactive ligand-receptor interaction

278

64

193

hsa05225

Hepatocellular carcinoma

168

56

112

hsa04020

Calcium signaling pathway

182

59

136

hsa04024

cAMP signaling pathway

198

58

139

hsa04217

Necroptosis

164

49

97

hsa04060

Cytokine-cytokine receptor interaction

270

70

192

hsa05152

Tuberculosis

179

58

112

hsa05165

Human papillomavirus infection

319

103

210

hsa04810

Regulation of actin cytoskeleton

208

64

132

hsa04151

PI3K-Akt signaling pathway

352

119

241

hsa04022

cGMP-PKG signaling pathway

163

58

109

hsa04630

Jak-STAT signaling pathway

162

43

112

hsa05167

Kaposi’s sarcoma-associated herpesvirus infection

186

61

114

hsa04010

MAPK signaling pathway

295

87

209

hsa04371

Apelin signaling pathway

137

46

99

hsa04390

Hippo signaling pathway

154

58

100

Neuroblastoma

hsa04976

Bile secretion

71

13

5

hsa05034

Alcoholism

180

22

7

hsa01100

Metabolic pathways

1273

43

93

hsa04080

Neuroactive ligand-receptor interaction

278

21

24

hsa04151

PI3K-Akt signaling pathway

352

19

31