Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer

BMC Cancer

Table 2 Top 20 pathways in the 500 signatures of ER-positive and ER-negative tumors evaluated by Global Test

Pathways	GO_ID	P	Frequency
ER-positive tumors
Apoptosis	6915	3.06E-7	250
Regulation of cell cycle	74	2.46E-5	203
Protein amino acid phosphorylation	6468	2.48E-5	114
Cytokinesis	910	6.13E-5	165
Cell motility	6928	0.00015	93
Cell cycle	7049	0.00028	138
Cell surface receptor-linked signal transd.	7166	0.00033	172
Mitosis	7067	0.00036	256
Intracellular protein transport	6886	0.00054	141
Mitotic chromosome segregation	70	0.00057	98
Ubiquitin-dependent protein catabolism	6511	0.00074	158
DNA repair	6281	0.00079	156
Induction of apoptosis	6917	0.00083	115
Immune response	6955	0.00094	167
Protein biosynthesis	6412	0.0010	145
DNA replication	6260	0.0015	92
Oncogenesis	7048	0.0020	228
Metabolism	8152	0.0021	83
Cellular defense response	6968	0.0025	131
Chemotaxis	6935	0.0027	89
ER-negative tumors
Regulation of cell growth	1558	0.00012	136
Regul. of G-coupled receptor signaling	8277	0.00013	153
Skeletal development	1501	0.00024	160
Protein amino acid phosphorylation	6468	0.0051	151
Cell adhesion	7155	0.0065	110
Carbohydrate metabolism	5975	0.0066	86
Nuclear mRNA splicing, via spliceosome	398	0.0067	203
Signal transduction	7165	0.0078	160
Cation transport	6812	0.0098	160
Calciumion transport	6816	0.010	93
Protein modification	6464	0.011	132
Intracellular signaling cascade	7242	0.012	135
mRNA processing	6397	0.012	81
RNA splicing	8380	0.014	192
Endocytosis	6897	0.026	166
Regul. of transcription from PolII promoter	6357	0.031	109
Regulation of cell cycle	74	0.043	88
Protein complex assembly	6461	0.048	183
Protein biosynthesis	6412	0.063	99
Cell cycle	7049	0.084	72

Each of the top 20 over-represented pathways that have the highest frequencies in the 500 signatures of ER-positive and ER-negative tumors were subjected to Global Test program [12, 14]. The Global Test examines the association of a group of genes as a whole to a specific clinical parameter, in this case DMFS, and generates an asymptotic theory p value for the pathway. The pathways are ranked by their p value in the respective ER-subgroup of tumors.

ISSN: 1471-2407