A comparative study on gene-set analysis methods for assessing differential expression associated with the survival phenotype

Lee, Seungyeoun; Kim, Jinheum; Lee, Sunho

doi:10.1186/1471-2105-12-377

Table 3 Pathways with more genes associated with overall survival as identified by either GT or WT at the nominal 0.01 level of the permutation test

From: A comparative study on gene-set analysis methods for assessing differential expression associated with the survival phenotype

Pathway name	Gene set size	p-value				q-value
		GSEA1	GSEA2	GT	WT GBST	GSEA1	GSEA2	GT	WT GBST
Pentose phosphate pathway	39	0.010	0.003	0.000	0.000 0.003	0.921	0.612	0.000	0.000 0.087
Histidine metabolism	54	0.070	0.012	0.000	0.000 0.000	0.921	0.638	0.000	0.000 0.000
Tryptophan metabolism	86	0.034	0.024	0.002	0.003 0.009	0.921	0.701	0.061	0.085 0.140
One carbon pool by folate	28	0.065	0.027	0.010	0.000 0.010	0.921	0.701	0.108	0.000 0.140
DNA replication	52	0.021	0.013	0.009	0.002 0.037	0.921	0.638	0.108	0.077 0.207
Colorectal cancer	165	0.139	0.145	0.003	0.010 0.000	0.921	0.811	0.073	0.136 0.000
Nucleotide excision repair	56	0.047	0.068	0.014	0.003 0.054	0.921	0.811	0.129	0.085 0.253
Urea cycle and metabolism of amino groups	40	0.031	0.259	0.010	0.036 0.003	0.921	0.878	0.108	0.191 0.087
Purine metabolism	201	0.081	0.026	0.003	0.009 0.072	0.921	0.701	0.074	0.136 0.275
Aminophosphonate metabolism	21	0.267	0.028	0.000	0.009 0.056	0.921	0.701	0.000	0.136 0.253
Pantothenate and CoA biosynthesis	19	0.252	0.061	0.189	0.010 0.003	0.921	0.811	0.337	0.136 0.087
Leukocyte transendothelial migration	197	0.332	0.161	0.004	0.013 0.003	0.921	0.811	0.074	0.166 0.087
Inositol metabolism	7	0.234	0.274	0.035	0.044 0.004	0.921	0.878	0.207	0.204 0.089
Tyrosine metabolism	81	0.531	0.147	0.017	0.018 0.003	0.970	0.811	0.133	0.171 0.087
Lysine degradation	56	0.124	0.225	0.004	0.018 0.137	0.921	0.878	0.074	0.171 0.362
Starch and sucrose metabolism	72	0.373	0.133	0.002	0.033 0.250	0.928	0.811	0.068	0.191 0.427
Glycerophospholipid metabolism	89	0.535	0.255	0.004	0.028 0.036	0.970	0.878	0.074	0.190 0.207
Androgen and estrogen metabolism	53	0.386	0.168	0.005	0.035 0.147	0.935	0.811	0.085	0.191 0.372
Jak-STAT signaling pathway	240	0.258	0.606	0.001	0.036 0.121	0.921	0.892	0.051	0.191 0.358
Starch and sucrose metabolism	72	0.373	0.133	0.002	0.033 0.250	0.928	0.811	0.068	0.191 0.427

Note: The underlined pathways are identified by Crijns et al.(2009).

Back to article page