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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