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Table 1 Top five upregulated and downregulated KEGG gene sets by gene set enrichment analysis

From: Assessing breast cancer cell lines as tumour models by comparison of mRNA expression profiles

KEGG gene set Mean t statistic Set size Mean correlation to stromal score Mean correlation to immune score Mean correlation to tumour purity
Upregulated sets      
 hsa03030 DNA replication 3.13 35 −0.27 −0.05 −0.18
 hsa04110 Cell cycle 2.85 113 −0.10 0.06 −0.01
 hsa03013 RNA transport 2.34 130 −0.13 0.00 −0.07
 hsa03008 Ribosome biogenesis in eukaryotes 2.30 61 −0.16 0.02 −0.08
 hsa03040 Spliceosome 2.06 103 −0.09 −0.04 −0.07
Downregulated sets
 hsa04512 ECM–receptor interaction −3.66 81 0.49 0.11 0.33
 hsa04514 Cell adhesion molecules −3.57 120 0.33 0.30 0.36
 hsa04610 Complement and coagulation cascades −3.57 67 0.49 0.34 0.46
 hsa04380 Osteoclast differentiation −3.41 117 0.44 0.49 0.53
 hsa04145 Phagosome −3.35 126 0.37 0.38 0.43
  1. Abbreviations: KEGG Kyoto Encyclopedia of Genes and Genomes
  2. GAGE mean t statistic and gene set size are reported for the top five up- and downregulated pathways as determined by gene set enrichment analysis. Stromal and immune correlations were calculated for each set’s essential genes and averaged for the entire pathway to provide an estimate of stromal and immune contribution to gene set perturbation