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