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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.