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Table 1 P-values for top 30 gene sets discovered by the integrative method using the competitive gene sets test

From: Integrating diverse genomic data using gene sets

Pathway

E1

E2

C1

C2

INT

AMINOSUGARS_METABOLISM*

0.0132

0.4429

0.4686

0.0085

0.0008

STREPTOMYCIN_BIOSYNTHESIS

0.1180

0.0822

0.8774

0.1301

0.0024

STARCH_AND_SUCROSE_METABOLISM*

0.0163

0.0457

0.6400

0.7045

0.0048

TRANSLATION_FACTORS

0.0006

0.0007

0.0700

0.0505

0.0092

HSA00860_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM

0.0034

0.1760

0.1306

0.1287

0.0098

GLYCOLYSISPATHWAY*

0.1321

0.2590

0.1119

0.0716

0.0105

HSA00624_1_AND_2_METHYLNAPHTHALENE_DEGRADATION

0.0157

0.0037

0.3096

0.4940

0.0115

HSA03050_PROTEASOME

< 10-4

0.0021

0.7431

0.9031

0.0123

HSA00521_STREPTOMYCIN_BIOSYNTHESIS

0.1243

0.1364

0.9467

0.2227

0.0124

HSA00530_AMINOSUGARS_METABOLISM*

0.0123

0.2232

0.8209

0.2205

0.0130

FRUCTOSE_AND_MANNOSE_METABOLISM*

0.2724

0.6586

0.2115

0.0618

0.0140

STRESSPATHWAY

0.3783

0.0589

0.0636

0.0533

0.0175

HSA00500_STARCH_AND_SUCROSE_METABOLISM*

0.0328

0.3084

0.7397

0.8215

0.0188

HSA00740_RIBOFLAVIN_METABOLISM

0.3108

0.1873

0.6021

0.1767

0.0198

PORPHYRIN_AND_CHLOROPHYLL_METABOLISM

0.0444

0.1849

0.3903

0.0703

0.0206

HSA00603_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GLOBOSERIES

0.3816

0.4798

0.2583

0.1846

0.0230

KREBS_TCA_CYCLE

0.3707

0.0663

0.3670

0.0117

0.0246

IL10PATHWAY

0.0391

0.0166

0.1396

0.0650

0.0263

BLOOD_GROUP_GLYCOLIPID_BIOSYNTHESIS_LACTOSERIES

0.0070

0.3230

0.4054

0.6334

0.0268

HSA00642_ETHYLBENZENE_DEGRADATION

0.0263

0.0198

0.1641

0.4937

0.0306

FEEDERPATHWAY*

0.1347

0.2727

0.2331

0.4541

0.0312

GALACTOSE_METABOLISM*

0.1987

0.2374

0.5055

0.0538

0.0333

CYTOKINEPATHWAY

0.0238

0.0439

0.1226

0.2484

0.0400

WNTPATHWAY

0.8890

0.2008

0.3227

0.0549

0.0402

HSA00051_FRUCTOSE_AND_MANNOSE_METABOLISM*

0.5893

0.7157

0.3759

0.0078

0.0408

GLYCOSAMINOGLYCAN_DEGRADATION*

0.0135

0.4210

0.0348

0.0208

0.0464

GLUCONEOGENESIS*

0.1634

0.0849

0.7657

0.5843

0.0488

GLYCOLYSIS*

0.1634

0.0849

0.7657

0.5843

0.0488

PROTEASOMEPATHWAY

0.0015

0.0702

0.6308

0.7039

0.0497

HSA00052_GALACTOSE_METABOLISM*

0.2507

0.4202

0.5990

0.0354

0.0497

  1. The sets discovered using integration but not using any of the single-data-type analyses are in bold font. An asterisk denotes sets related to sugar metabolic processes. Discoveries are sets whose P-value is < 0.05. E1 and E2, single data type analysis using expression data; C1 and C2, single data type analysis using copy number data; INT, integrative method.
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Genome Biology

ISSN: 1474-760X

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