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Table 2 Functional overview of top scoring modules

From: Using random walks to identify cancer-associated modules in expression data

Breast cancer

ID

Score

Size

Key functional annotation

134

40.20

16

DNA REPLICATION, ATR SIGNALING, CELL CYCLE, SYNTHESIS OF DNA, UNWINDING OF DNA

82

27.77

32

VEGF AND VEGFR SIGNALING, FOCAL ADHESION, CYTOKINE RECEPTOR INTERACTIONS, MTOR SIGNALING, PI3K CASCADE, ERBB SIGNALING, IRS SIGNALING, ANGIOGENESIS, FGFR SIGNALING, GLYPICAN1 NETWORK, SYNDECAN SIGNALING, IGF1 PATHWAY, ARF6 SIGNALING

226

21.26

16

NUCLEAR ESTROGEN RECEPTOR ALPHA NETWORK, REGULATION OF ANDROGEN RECEPTOR

224

19.08

27

METABOLISM OF NUCLEOTIDES, DNA REPLICATION, APOPTOSIS PATHWAY, ARF6 PATHWAY, CAM PATHWAY, TELOMERES EXTENSTION, PLC-G1 SIGNALING, GLUCAGON SIGNALING, C-MYC TRANSCRIPTION, GNRH SIGNALING, ERBB2 SIGNALING, EGFR SIGNALING IN CANCER

79

16.08

24

JAK-STAT SIGNALING, INTERFERON SIGNALING, CYTOKINE SIGNALING, GROWTH HORMONE RECEPTOR SIGNALING, LEPTIN SIGNALING, INSULIN SIGNALING, PROLACTIN SIGNALING, SIGNALING BY INTERLEUKINS, SHP2 SIGNALING, ERBB2 IN SIGNAL TRANSDUCTION AND ONCOLOGY, EPO SIGNALING, CD40/CD40L SIGNALING, EGFR SIGNALING, KIT SIGNALING

395

15.32

29

G ALPHA SIGNALING, GPCR SIGNALING, METABOLISM OF NUCLEOTIDES, CAM PATHWAY, SIGNALING BY ERBB2, SIGNALING BY EGFR IN CANCER, GROWTH FACTOR SIGNALING

182

14.59

12

FOXM1 TRANSCRIPTION, PROGESTERONE-MEDIATED OOCYTE MATURATION,

96

13.74

13

REELIN SIGNALING, GLYCOGEN METABOLISM, SIGNALING BY INTERLEUKINS, WNT SIGNALING, PHOSPHOINOSITIDE TARGETS, IFN-GAMMA PATHWAY, REGULATION OF MICROTUBULE CYTOSKELETON, TGF-BETA SIGNALING, KIT SIGNALING, SEMAPHORIN INTERACTIONS

321

10.99

5

VITAMIN A AND CAROTENOID METABOLISM, CYTOCHROME P450

145

10.97

11

CELL CYCLE, DNA DAMAGE RESPONSE, P53 SIGNALING, P38 MAPK SIGNALING, SONIC HEDGEHOG RECEPTOR, EFP CONTROLS CELL CYCLE AND BREAST TUMORS GROWTH, TGF BETA SIGNALING, INTEGRATED BREAST CANCER PATHWAY, MAPK SIGNALING, FOXM1 TRANSCRIPTION, AMPK SIGNALING

165

10.90

55

NUCLEAR ESTROGEN RECEPTOR NETWORK, ATF-2 TRANSCRIPTION, RETINOIC ACID RECEPTORS-MEDIATED SIGNALING, SIGNALING MEDIATED BY P38-ALPHA AND P38-BETA, FOXA1 TRANSCRIPTION

122

9.28

16

BCR SIGNALING, TCR SIGNALING, NATURAL KILLER CELL CYTOTOXICITY, FC EPSILON SIGNALING, PI3K SIGNALING, JNK SIGNALING, NF-KAPPA B SIGNALING, INTERLEUKIN SIGNALING, EPO SIGNALING, CDC42 REGULATION, EGF-EGFR SIGNALING, RAC1 REGULATION, REGULATION OF RHOA

143

8.97

11

SKP2 DEGRADATION OF P27/P21, FOXM1 TRANSCRIPTION, P73 TRANSCRIPTION, PRL SIGNALING, ATR SIGNALING, P53 PATHWAY, RB TUMOR SUPPRESSOR/CHECKPOINT, EFP CONTROLS CELL CYCLE/ BREAST TUMOR GROWTH, AKT SIGNALING, AHR PATHWAY, NOTCH SIGNALING, ERBB SIGNALING, PI3K CASCADE, AMPK SIGNALING, C-MYC TRANSCRIPTIONAL REPRESSION, SMAD2/3 SIGNALING

205

8.71

15

DNA DAMAGE RESPONSE, CELL CYCLE, INTEGRATED BREAST CANCER PATHWAY, WNT SIGNALING, AURORA A SIGNALING, LKB1 SIGNALING, C-MYC TRANSCRIPTION REGULATION, BARD1 SIGNALING, ATM PATHWAY, PLK3 SIGNALING, HEDGEHOG SIGNALING, ERBB SIGNALING, P53 PATHWAY, HTERT TRANSCRIPTIONAL REGULATION, VEGFR1/ VEGFR2 SIGNALING, AP-1 TRANSCRIPTION, E2F TRANSCRIPTION, BRCA1 BRCA2 AND ATR IN CANCER, ARF INHIBITS BIOGENESIS, NUCLEAR ESTROGEN RECEPTOR ALPHA NETWORK, AMPK SIGNALING

89

8.54

7

REGULATION OF IGF ACTIVITY BY INSULIN-LIKE GROWTH FACTOR BINDING PROTEINS

189

8.25

7

C-MYB TRANSCRIPTION, TRANSCRIPTIONAL MISREGULATION IN CANCER, AP-1 TRANSCRIPTION

348

8.20

29

REGULATION OF ACTIN CYTOSKELETON, SHC CASCADE, FGFR SIGNALING, MAPK SIGNALING, PHOSPHOLIPASE C CASCADE, PI3K CASCADE, IRS SIGNALING, INSULIN SIGNALING, SYNDECAN SIGNALING, ERBB SIGNALING, FOCAL ADHESION, ANGIOGENESIS

173

8.18

6

METABOLISM OF NUCLEOTIDES, DRUG METABOLISM, E2F TRANSCRIPTION

99

7.47

7

P38 SIGNALING MEDIATED BY MAPKAP KINASES, CELL CYCLE, INSULIN-MEDIATED GLUCOSE TRANSPORT, PI3K SIGNALING MEDIATED BY AKT, INTEGRIN SIGNALING, MTOR SIGNALING, BETA CATENIN SIGNALING, ERBB1 SIGNALING, PDGFR-BETA SIGNALING, SIGNALING BY HIPPO

12

7.25

23

MAPK SIGNALING, ATF-2 TRANSCRIPTION, REGULATION OF P38-ALPHA AND P38-BETA, TOLL LIKE RECEPTOR CASCADE, ERBB1 SIGNALING, NGF SIGNALING, RAS SIGNALING

Hepatocellular carcinoma

408

72.64

24

DRUG METABOLISM - CYTOCHROME P450, METABOLISM OF AMINO ACIDS, FATTY ACID METABOLISM GLYCOLYSIS/GLUCONEOGENESIS, ETHANOL OXIDATION, ARACHIDONIC ACID METABOLISM, TAMOXIFEN METABOLISM, VITAMIN A/CAROTENOID METABOLISM, ESTROGEN METABOLISM, AHR PATHWAY

10

34.22

49

DRUG METABOLISM, STEROID HORMONE BIOSYNTHESIS, RETINOL METABOLISM, CYTOCHROME P450 METABOLISM, METABOLISM OF AMINO ACIDS, TAMOXIFEN METABOLISM, FATTY ACID OXIDATION, BENZO(A)PYRENE METABOLISM, AHR PATHWAY, AFLATOXIN B1 METABOLISM, IL-10 SIGNALING

513

22.92

4

ALTERNATIVE COMPLEMENT PATHWAY, COMPLEMENT AND COAGULATION CASCADES

579

19.55

13

METABOLISM OF STEROID HORMONES AND VITAMINS A AND D, METABOLISM OF LIPIDS AND LIPOPROTEINS, MINERALOCORTICOID BIOSYNTHESIS, GLUCOCORTICOID METABOLISM

603

17.58

6

METABOLISM OF AMINO ACIDS

31

14.24

14

PPAR SIGNALING, FATTY ACID, TRIACYLGLYCEROL, AND KETONE BODY METABOLISM, ADIPOCYTOKINE SIGNALING, METABOLISM OF LIPIDS AND LIPOPROTEINS, AMPK SIGNALING

97

13.93

5

ONE CARBON POOL BY FOLATE, METABOLISM OF AMINO ACIDS AND DERIVATIVES

361

9.55

16

DNA REPLICATION, CELL CYCLE, UNWINDING OF DNA, SYNTHESIS OF DNA

314

9.47

10

FATTY ACID METABOLISM, GLYCEROLIPID METABOLISM, METABOLISM OF AMINO ACIDS

34

9.08

14

TOLL-LIKE RECEPTOR SIGNALING, HTLV-I INFECTION, ACTIVATION OF AP-1 TRANSCRIPTION FACTORS, MAPK SIGNALING, TWEAK SIGNALING, TGF BETA SIGNALING, INTERLEUKIN SIGNALING, RIG-I-LIKE RECEPTOR SIGNALING, HEPATITIS B VIRUS, IGF-1 SIGNALING, HEPATOCYTE GROWTH FACTOR RECEPTOR SIGNALING, JAK-STAT SIGNALING, FAS PATHWAY

598

8.94

4

KEAP1-NRF2 PATHWAY, METABOLISM OF AMINO ACIDS AND DERIVATIVES

360

8.73

7

INSULIN SIGNALING, GLYCOGEN METABOLISM, GLUCOSE METABOLISM, METABOLISM OF CARBOHYDRATES

112

8.65

5

MRNA SPLICING, MRNA PROCESSING

515

8.46

10

ONE CARBON POOL BY FOLATE, FOLATE METABOLISM

257

8.23

5

UREA CYCLE AND METABOLISM OF AMINO GROUPS, METABOLISM OF AMINO ACIDS

153

7.29

5

GLUCOCORTICOID & MINERALCORTICOID METABOLISM, METABOLISM OF STEROID HORMONES & VITA/D, METABOLISM OF LIPIDS & LIPOPROTEINS, PROSTAGLANDIN SYNTHESIS/ REGULATION

123

7.22

7

ONE CARBON FOLATE METABOLISM, METHYLATION, METABOLISM OF AMINO ACIDS

254

7.03

6

METABOLISM OF NUCLEOTIDES, METABOLISM OF AMINO ACIDS AND DERIVATIVES

429

7.02

9

SIGNAL TRANSDUCTION BY L1, MTOR SIGNALING, RSK ACTIVATION, PROSTATE CANCER, L1CAM INTERACTIONS, CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF RAS, MAPK SIGNALING

414

6.50

35

MAPK SIGNALING, ATF-2 TRANSCRIPTION, CELL SIGNALING IN H. PYLORI INFECTION, ACTIVATION OF AP-1 TRANSCRIPTION FACTORS, FC EPSILON RI SIGNALING, NOD1/2 SIGNALING, GNRH SIGNALING, JNK SIGNALING, CD40/CD40L SIGNALING, C RIG-I-LIKE RECEPTOR SIGNALING, TGF BETA SIGNALING, VEGF SIGNALING, EGF-EGFR SIGNALING, FOSB GENE EXPRESSION

Colorectal adenoma

257

33.48

50

CHEMOKINE SIGNALING, GPCR SIGNALING, NF-KAPPA B SIGNALING, CXCR3 SIGNALING, TOLL-LIKE RECEPTOR SIGNALING, NOD-LIKE RECEPTOR SIGNALING, INTESTINAL IMMUNE NETWORK FOR IGA PRODUCTION, INTERLEUKIN SIGNALING, CELL SIGNALING IN H. PYLORI INFECTION

182

21.57

25

TIGHT JUNCTION INTERACTIONS, TRANSENDOTHELIAL MIGRATION, CELL-CELL COMMUNICATION, CAMS

158

18.94

9

P75(NTR) SIGNALING, DEGRADATION OF THE ECM, ECM ORGANIZATION, SYNDECAN SIGNALING

770

12.58

8

ETHANOL OXIDATION, METABOLISM BY CYTOCHROME P450, TYROSINE METABOLISM, FATTY ACID METABOLISM, GLYCOLYSIS/GLUCONEOGENESIS, VITAMIN A/CAROTENOID METABOLISM

14

11.51

5

C-MYC TRANSCRIPTIONAL REPRESSION, SMAD2/3 SIGNALING, CELL CYCLE, PATHWAYS IN CANCER

452

8.75

10

GLYCOSPHINGOLIPID BIOSYNTHESIS, GLYCOSAMINOGLYCAN BIOSYNTHESIS

487

7.16

28

MAPK SIGNALING, ATF-2 TRANSCRIPTION, ACTIVATION OF AP-1 TRANSCRIPTION FACTORS, NOD-LIKE RECEPTOR SIGNALING, FC EPSILON SIGNALING, GNRH SIGNALING, TOLL-LIKE RECEPTOR SIGNALING, INTERLEUKIN SIGNALING, TGF BETA SIGNALING, VEGF SIGNALING, EGF-EGFR SIGNALING, KIT SIGNALING, RANKL-RANK SIGNALING, COLORECTAL CANCER, S1P2 PATHWAY, NONCANONICAL WNT SIGNALING, ARF6 PATHWAY, ERBB SIGNALING, TBXA2R SIGNALING

301

7.06

7

TRANSCRIPTIONAL MISREGULATION IN CANCER, RB REGULATION, INTERLEUKIN SIGNALING, C-MYB TRANSCRIPTION, INTERFERON SIGNALING, FOXA2/ FOXA3 TRANSCRIPTIONS, SMAD2/3 SIGNALING

758

6.91

5

METABOLISM OF AMINO ACIDS AND DERIVATIVES

762

6.59

12

WNT SIGNALING, SECRETIN FAMILY OF RECEPTORS, HTLV-I INFECTION, SIGNALING BY GPCR

240

6.59

28

G PROTEIN SIGNALING, CAM PATHWAY, PLC-GAMMA1 SIGNALING, NUCLEOTIDE METABOLISM, SIGNALING BY ERBB2, SIGNALING BY EGFR, SIGNALING BY FGFR, SIGNALING BY PDGF

757

6.53

12

METABOLISM OF STEROID HORMONES AND VITA/D, METABOLISM OF LIPIDS AND LIPOPROTEINS, GLUCOCORTICOID & MINERALCORTICOID METABOLISM, BILE ACID AND BILE SALT METABOLISM

410

6.49

6

JAK-STAT SIGNALING, CYTOKINE-CYTOKINE RECEPTOR INTERACTION, SHP2 SIGNALING, INTERLEUKIN SIGNALING, ROLE OF ERBB2 IN SIGNAL TRANSDUCTION AND ONCOLOGY

412

6.21

9

DNA REPLICATION, CELL CYCLE, UNWINDING OF DNA, ATR SIGNALING, E2F TRANSCRIPTION

345

6.13

14

NEUROTROPHIN SIGNALING, GNRH SIGNALING, CREB PHOSPHORYLATION, PKA ACTIVATION, CAM PATHWAY, INSULIN SIGNALING, PGC-1A REGULATION, RAS REGULATION, SMAD2/3 SIGNALING

267

6.06

6

METABOLISM OF PROTEINS

334

6.04

12

BETA-CATENIN PHOSPHORYLATION CASCADE, SIGNALING BY WNT, GLYCOGEN METABOLISM, PLATELET HOMEOSTASIS, DNA REPLICATION, CELL CYCLE, DNA DAMAGE RESPONSE

111

5.74

11

ECM-RECEPTOR INTERACTION, FOCAL ADHESION, INTEGRIN INTERACTIONS, NCAM INTERACTIONS, SYNDECAN SIGNALING, PROTHROMBIN ACTIVATION PATHWAY, PDGF SIGNALING, VEGFR3 SIGNALING

54

5.73

4

NONE

125

5.67

20

CHEMOKINE SIGNALING, G ALPHA SIGNALING, SIGNALING BY GPCR, ACTIVATION OF PKA, INTESTINAL IMMUNE NETWORK FOR IGA, CELL SIGNALING IN HELICOBACTER PYLORI INFECTION

183

5.41

6

BETA-CATENIN PHOSPHORYLATION CASCADE, CTLA4 INHIBITORY SIGNALING, GLYCOGEN METABOLISM, WNT SIGNALING, DNA REPLICATION, CELL CYCLE, IMMUNE SYSTEM, DNA DAMAGE RESPONSE

156

5.38

4

HEMATOPOIETIC CELL LINEAGE

144

5.35

16

CELL CYCLE, P38/MAPKAP SIGNALING, LKB1 SIGNALING, INSULIN-MEDIATED GLUCOSE TRANSPORT, PI3K/AKT SIGNALING, INTEGRIN SIGNALING, FOXO FAMILY SIGNALING, MTOR SIGNALING, ERBB1 SIGNALING, PDGFR-BETA SIGNALING, ATR SIGNALING, PLK1 SIGNALING, RB TUMOR SUPPRESSOR/CHECKPOINT, RAP1 SIGNALING, INTEGRATED CANCER PATHWAY, ATM PATHWAY, SHC SIGNALING, ARMS-MEDIATED ACTIVATION, IGF1 PATHWAY, IRS SIGNALING