Skip to main content

Table 2 P-values for top 30 gene sets discovered by the integrative method using the self-contained gene sets test

From: Integrating diverse genomic data using gene sets

Pathway

E1

E2

C1

C2

INT

INT for validation set

HSA04810_REGULATION_OF_ACTIN_CYTOSKELETON

0.0697

0.2250

< 10-4

< 10-4

< 10-4

0.0001

HSA04010_MAPK_SIGNALING_PATHWAY

0.1302

0.0746

< 10-4

< 10-4

< 10-4

< 10-4

HSA04060_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION

0.1422

0.0132

< 10-4

< 10-4

< 10-4

0.0147

HSA04310_WNT_SIGNALING_PATHWAY

0.2389

0.0039

< 10-4

< 10-4

< 10-4

0.0001

HSA04080_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION

0.1164

0.8695

0.0001

0.0005

< 10-4

0.0042

HSA00230_PURINE_METABOLISM

0.0034

0.0503

0.0000

0.0003

< 10-4

0.0022

TRANSLATION_FACTORS

0.0208

0.0155

0.0022

0.0052

0.0001

0.2711

HSA01030_GLYCAN_STRUCTURES_BIOSYNTHESIS_1

0.0781

0.0292

0.0004

0.0003

0.0001

0.0454

HSA04360_AXON_GUIDANCE

0.4293

0.1803

< 10-4

0.0106

0.0001

0.0001

GLUCONEOGENESIS*

0.0435

0.1010

0.0613

0.0106

0.0001

0.0409

GLYCOLYSIS*

0.0435

0.1010

0.0613

0.1065

0.0001

0.0409

HSA00500_STARCH_AND_SUCROSE_METABOLISM*

0.0448

0.2669

0.0140

0.0043

0.0001

0.0364

HSA04630_JAK_STAT_SIGNALING_PATHWAY

0.2975

0.0090

0.0022

0.0041

0.0002

0.0141

HSA04510_FOCAL_ADHESION

0.0423

0.0926

0.0042

0.0374

0.0002

10-4

MRNA_PROCESSING_REACTOME

0.1660

0.0062

0.0537

0.0004

0.0003

< 10-4

HSA05215_PROSTATE_CANCER

0.0534

0.3618

0.0013

0.0534

0.0004

0.0008

HSA01031_GLYCAN_STRUCTURES_BIOSYNTHESIS_2

0.0084

0.0076

0.0312

0.0141

0.0004

0.0926

HSA00240_PYRIMIDINE_METABOLISM

0.0013

0.0307

0.0022

0.0065

0.0004

0.0063

HSA04210_APOPTOSIS

0.1207

0.2064

0.0003

0.0001

0.0004

0.0021

HSA04620_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY

0.1986

0.1228

0.0001

0.0109

0.0004

0.0006

GLYCOLYSIS_AND_GLUCONEOGENESIS*

0.0209

0.1407

0.0476

0.0112

0.0005

0.1808

HSA04660_T_CELL_RECEPTOR_SIGNALING_PATHWAY

0.0192

0.1176

0.0141

0.0027

0.0006

0.0661

HSA00051_FRUCTOSE_AND_MANNOSE_METABOLISM*

0.1565

0.2238

0.0314

0.0112

0.0006

0.2631

HSA00010_GLYCOLYSIS_AND_GLUCONEOGENESIS*

0.0515

0.1333

0.1276

0.0148

0.0007

0.0647

INTEGRIN_MEDIATED_CELL_ADHESION_KEGG

0.2779

0.1734

0.0017

0.0038

0.0007

0.0001

HSA04640_HEMATOPOIETIC_CELL_LINEAGE

0.0634

0.0676

0.0140

0.0009

0.0007

0.0026

GPCRDB_CLASS_A_RHODOPSIN_LIKE

0.3429

0.4710

0.0003

0.0483

0.0008

0.0449

HSA00350_TYROSINE_METABOLISM

0.0219

0.0421

0.0772

0.0085

0.0008

0.0648

HSA05221_ACUTE_MYELOID_LEUKEMIA

0.0697

0.3196

0.0213

0.0105

0.0009

0.0310

CALCINEURIN_NF_AT_SIGNALING

0.1302

0.1298

0.0205

0.0005

0.0010

0.1128

  1. Asterisks indicate sets related to sugar metabolic processes. E1 and E2, single data type analysis using expression data; C1 and C2, single data type analysis using copy number data; INT, integrative method.