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

Breast Cancer Research

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

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

Abbreviations: KEGG Kyoto Encyclopedia of Genes and Genomes
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

ISSN: 1465-542X