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Table 2 Metastatic pathways identified by gene set enrichment meta-analysis.

From: Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer

Pathway Ams Hua HUM Rot S03 S06 Sto Upp mean p FDR
Up-regulated            
DNA_REPLICATION_REACTOME 11 64 2 19 5 6 2 6 14.4 < 10E-6 < 10E-6
CELL_CYCLE_KEGG 4 101 1 14 39 5 3 12 22.4 1.0E-6 1.1E-4
ATRBRCAPATHWAY 58 10 23 1 73 41 9 17 29.0 2.2E-5 1.5E-3
AMINOACYL_TRNA_BIOSYNTHESIS 35 90 57 21 9 9 8 10 29.9 2.7E-5 1.5E-3
PYRIMIDINE_METABOLISM 5 9 11 20 159 3 7 34 31.0 3.5E-5 1.6E-3
G1_TO_S_CELL_CYCLE_REACTOME 22 141 5 5 65 19 5 11 34.1 8.2E-5 3.0E-3
PROTEASOME_DEGRADATION 29 128 71 29 2 13 1 7 35.0 1.0E-4 3.0E-3
G2PATHWAY 30 107 4 23 86 8 15 9 35.3 1.1E-4 3.0E-3
PROTEASOMEPATHWAY 36 155 45 10 1 14 10 16 35.9 1.3E-4 3.1E-3
PURINE_METABOLISM 23 70 54 38 57 22 22 28 39.3 2.7E-4 6.0E-3
MRNA_PROCESSING_REACTOME 59 67 68 34 14 53 23 20 42.3 5.0E-4 1.0E-2
PROTEASOME 38 171 18 31 3 50 12 26 43.6 6.6E-4 1.2E-2
VEGFPATHWAY 41 52 84 4 37 38 81 13 43.8 6.8E-4 1.2E-2
PENTOSE_PHOSPHATE_PATHWAY 28 140 83 68 10 17 4 3 44.1 7.3E-4 1.2E-2
CELLCYCLEPATHWAY 44 112 3 13 139 2 27 21 45.1 8.7E-4 1.3E-2
GLYCOLYSIS_AND_GLUCONEOGENESIS 1 145 107 62 4 10 16 24 46.1 1.1E-3 1.5E-2
OXIDATIVE_PHOSPHORYLATION 80 142 25 15 85 16 11 1 46.9 1.2E-3 1.6E-2
G1PATHWAY 75 39 27 11 171 25 36 8 49.0 1.7E-3 2.0E-2
ARAPPATHWAY 19 8 175 17 49 43 25 56 49.0 1.7E-3 2.0E-2
FRUCTOSE_AND_MANNOSE_METABOLISM 10 11 145 41 58 101 19 14 49.9 2.0E-3 2.3E-2
S1P_SIGNALING 17 35 60 25 131 66 51 22 50.9 2.4E-3 2.5E-2
ACTINYPATHWAY 6 219 50 2 15 60 24 43 52.4 3.0E-3 3.1E-2
ELECTRON_TRANSPORT_CHAIN 131 191 36 9 41 12 6 5 53.9 3.8E-3 3.7E-2
RNA_TRANSCRIPTION_REACTOME 133 69 6 24 97 49 37 19 54.3 4.0E-3 3.7E-2
MPRPATHWAY 26 176 12 28 129 1 20 44 54.5 4.2E-3 3.7E-2
UBIQUITIN_MEDIATED_PROTEOLYSIS 46 125 128 89 6 15 14 15 54.8 4.3E-3 3.7E-2
Down-regulated            
HISTIDINE_METABOLISM 193 151 117 189 184 191 145 212 172.8 2.5E-3 4.6E-2
PPARAPATHWAY 192 167 131 177 168 133 206 210 173.0 2.4E-3 4.6E-2
GLYCEROLIPID_METABOLISM 165 85 204 207 221 185 155 177 174.9 1.8E-3 4.0E-2
FATTY_ACID_METABOLISM 164 210 176 138 200 140 163 211 175.3 1.7E-3 4.0E-2
PDGFPATHWAY 209 127 182 185 112 181 212 213 177.6 1.1E-3 3.1E-2
EGFPATHWAY 208 124 192 191 106 197 190 215 177.9 1.1E-3 3.1E-2
NUCLEAR_RECEPTORS 173 202 121 174 199 150 214 193 178.3 9.8E-4 3.1E-2
BETA_ALANINE_METABOLISM 218 164 116 165 218 163 193 203 180.0 7.2E-4 3.1E-2
TOLLPATHWAY 212 119 167 204 128 223 165 222 180.0 7.2E-4 3.1E-2
GPCRDB_OTHER 134 196 164 158 210 196 205 195 182.3 4.5E-4 3.1E-2
GLEEVECPATHWAY 219 73 177 219 203 166 199 219 184.4 2.9E-4 3.1E-2
VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 222 174 184 181 207 194 97 217 184.5 2.8E-4 3.1E-2
  1. The ranking numbers indicate the ranking of each gene set (pathway) out of the 223 gene sets in each data set and the mean ranking number indicate the ranking in the meta-analysis. Only 38 significant out of a total of 223 gene sets are shown. Ams: Amsterdam, Hua: Huang, HUM: HUMAC, Rot: Rotterdam, S03: Sotiriou 2003, S06: Sotiriou 2006, Sto: Stockholm, Upp: Uppsala.