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Table 1 p values for the 50 Hallmarks gene sets. p values were calculated using the 294 sample cohort using ES, ESavg or < ESavg > with 25 splits as the test statistic. Gene sets are sorted by increasing p value obtained using ESavg as the statistic

From: Improving the power of gene set enrichment analyses

Gene Set

p value with ES

p value with ESavg

p value with <ESavg>

MTORC1_SIGNALING

< 0.0001

< 0.0001

< 0.0001

E2F_TARGETS

< 0.0001

< 0.0001

< 0.0001

UV_RESPONSE_UP

0.0132

< 0.0001

< 0.0001

G2M_CHECKPOINT

< 0.0001

< 0.0001

< 0.0001

PI3K_AKT_MTOR_SIGNALING

0.0040

0.0002

< 0.0001

MITOTIC_SPINDLE

0.0028

0.0004

< 0.0001

UNFOLDED_PROTEIN_RESPONSE

0.0006

0.0004

< 0.0001

REACTIVE_OXIGEN_SPECIES_PATHWAY

0.0063

0.0004

0.0002

ESTROGEN_RESPONSE_EARLY

0.0068

0.0006

0.0002

SPERMATOGENESIS

0.0185

0.0006

0.0002

GLYCOLYSIS

0.0216

0.0012

0.0008

MYC_TARGETS_V1

0.0172

0.0020

0.0002

UV_RESPONSE_DN

0.0156

0.0020

0.0012

MYC_TARGETS_V2

0.0320

0.0032

0.0026

DNA_REPAIR

0.0263

0.0035

0.0008

INTERFERON_GAMMA_RESPONSE

0.0373

0.0046

0.0038

IL6_JAK_STAT3_SIGNALING

0.0790

0.0074

0.0081

INTERFERON_ALPHA_RESPONSE

0.0638

0.0080

0.0105

COMPLEMENT

0.1059

0.0157

0.0149

ESTROGEN_RESPONSE_LATE

0.0622

0.0188

0.0080

ALLOGRAFT_REJECTION

0.0684

0.0194

0.0144

INFLAMMATORY_RESPONSE

0.0963

0.0303

0.0172

CHOLESTEROL_HOMEOSTASIS

0.1035

0.0449

0.0252

BILE_ACID_METABOLISM

0.0966

0.0472

0.0247

ANGIOGENESIS

0.2591

0.0796

0.0753

WNT_BETA_CATENIN_SIGNALING

0.4422

0.1160

0.1235

EPITHELIAL_MESENCHYMAL_TRANSITION

0.2984

0.1219

0.0984

COAGULATION

0.2516

0.1223

0.1093

IL2_STAT5_SIGNALING

0.1685

0.1437

0.0596

MYOGENESIS

0.2767

0.1589

0.1043

TGF_BETA_SIGNALING

0.3229

0.1593

0.1344

OXIDATIVE_PHOSPHORYLATION

0.3773

0.1877

0.1604

PROTEIN_SECRETION

0.3107

0.2032

0.2028

ADIPOGENESIS

0.4204

0.2247

0.2581

APICAL_SURFACE

0.4078

0.2477

0.0824

P53_PATHWAY

0.5724

0.2489

0.2423

TNFA_SIGNALING_VIA_NFKB

0.3401

0.2509

0.1545

HYPOXIA

0.4398

0.2712

0.2450

APOPTOSIS

0.5796

0.2905

0.3886

APICAL_JUNCTION

0.5175

0.2907

0.2579

NOTCH_SIGNALING

0.7451

0.3104

0.3226

FATTY_ACID_METABOLISM

0.5358

0.3134

0.3853

PANCREAS_BETA_CELLS

0.6834

0.3201

0.1500

XENOBIOTIC_METABOLISM

0.4921

0.3541

0.4946

HEME_METABOLISM

0.7713

0.4576

0.4731

KRAS_SIGNALING_UP

0.6241

0.7068

0.4892

ANDROGEN_RESPONSE

0.8082

0.7539

0.5841

HEDGEHOG_SIGNALING

0.7870

0.7810

0.5163

PEROXISOME

0.3931

0.8977

0.3682

KRAS_SIGNALING_DN

0.9700

0.9193

0.7337

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BMC Bioinformatics

ISSN: 1471-2105

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