Table 2. Association between the inferred TP53 mutation status-specific signatures with previously reported EMT and stemness markers. Statistical significance of differential expressed geneset overlapping the stemness and epithelial-mesenchymal transition (EMT) marker genelistsa. Statistical significance was computed by applying hypergeometric testb.
| wtTP53 signature | Mutant TP53 signature | Top 1000 genes ranked acc to absolute SNR (wt vs mtTP53 BC) | Top 1000 mt TP53 -upregulated genes ranked acc to SNR | |||||
|---|---|---|---|---|---|---|---|---|
| EMT and stemness geneset and its transcript size | Number of overlapping genes | P -value | Number of overlapping genes | P -value | Number of overlapping genes | P -value | Number of overlapping genes | P -value |
| EMT (n=497) | 0 | NS | 1 | NS | 11 | NS | 15 | 0.031 |
| ESC (n=553) | 0 | NS | 14 | 2.65E−13 | 22 | 2.60E−04 | 35 | 4.34E−11 |
| PRC2 (n=1016) | 7 | 3.25E−03 | 0 | NS | 25 | NS | 19 | NS |
| iPSC (n=597) | 1 | NS | 3 | NS | 17 | 4.50E−02 | 22 | 1.50E−03 |
| p53esc (n=912) | 2 | NS | 5 | 2.66E−02 | 12 | NS | 15 | NS |
Abbreviations: BC, breast cancer; ESC, embryonic stem cell; iPSC, induced pluripotent stem cell; NS, not significant; p53esc, p53 targets identified in murine embryonic stem cells; PRC2, polycomb repressive complex 2; SNR, signal-to-noise ratio.
a
Sources of the genelists are described in the Supplementary Table 6A.
b
Statistical significance was evaluated by Fisher’s exact test, in instances where number of overlapping genes ⩽5.