Table 5.
Marker gene enrichment analysis
|
Cluster |
Marker gene |
Marker gene |
#C |
#M |
#(C∩M) |
p |
|---|---|---|---|---|---|---|
| description | reference | |||||
| 1 |
IAC |
Celis et al. [37] |
11 |
32 |
5 |
3.3E-11 |
| 2 |
HER2+ |
Staaf et al. [39] |
12 |
15 |
4 |
6.2E-10 |
| 3 |
AR responsive |
Doane et al. [40] |
47 |
70 |
19 |
5.2E-32 |
| 5 | FOXC1 subtype | Ray et al. [41] | 13 | 17 | 3 | 5.6E-07 |
Analysis of the genes identified by DCglob that showed higher correlation in ER- compared to ER+ breast cancer. The gene clusters (C) were compared to lists of marker genes (M) from the literature. Let #C denote the number of genes in the clusters, #M the number of marker genes and #(C ∩M) the number of genes in the intersection. The significance of enrichment was assessed using Fisher’s exact test. IAC invasive apocrine carcinomas, AR androgen receptor.