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Table 7 Top scoring gene sets resulting from the analysis of the Hedenfalk data.

From: A general modular framework for gene set enrichment analysis

  Gene set p-value
1 breast_cancer_estrogen_signalling 0.000
2 cell_surface_receptor_linked_signal_transduction 0.000
3 insulin_signalling 0.000
4 p53_signalling 0.000
5 pparaPathway 0.000
6 VOXPHOS 0.000
7 RAP_UP 0.000
8 PROLIF_GENES 0.000
9 UPREG_BY_HOXA9 0.000
10 cell_adhesion 0.001
11 CR_CAM 0.001
12 CR_DEATH 0.001
13 il2rbPathway 0.001
14 ST_Tumor_Necrosis_Factor_Pathway 0.001
15 tcrPathway 0.001
16 HTERT_UP 0.001
17 CBF_LEUKEMIA_DOWNING_AML 0.001
18 CR_SIGNALLING 0.002
19 ghPathway 0.002
20 ST_B_Cell_Antigen_Receptor 0.002
21 tpoPathway 0.002
22 GO_0005739 0.002
23 LEU_UP 0.002
24 Cell_Cycle 0.003
25 GLUT_UP 0.003
26 FRASOR_ER_DOWN 0.003
27 ANDROGEN_UP_GENES 0.003
28 fmlppathway 0.004
29 hivnefPathway 0.004
30 biopeptidesPathway 0.005
31 cell_adhesion_molecule_activity 0.005
32 SIG_InsulinReceptorPathwayInCardiacMyocytes 0.005
33 ST_Integrin_Signaling_Pathway 0.005
34 drug_resistance_and_metabolism 0.006
35 ST_Differentiation_Pathway_in_PC12_Cells 0.007
36 gleevecPathway 0.008
37 DNA_DAMAGE_SIGNALLING 0.009
38 ST_ERK1_ERK2_MAPK_Pathway 0.009
39 mRNA_splicing 0.010
40 nfatPathway 0.010
41 HUMAN_CD34_ENRICHED_TF_JP 0.010
  1. As gene set statistic we used the mean combined with the squared moderated t- statistic on the gene level and sample label permutation.