A general modular framework for gene set enrichment analysis

BMC Bioinformatics

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

	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

As gene set statistic we used the mean combined with the squared moderated t- statistic on the gene level and sample label permutation.

ISSN: 1471-2105