TABLE 2.
Upstream regulator analysis of TCGA breast cancer data identifies patient group-associated TFs that have a common association with ATAC-seq signals in the TNBC human cell lines
| Upstream Regulator Analysis using TCGA RNA-seq Dataa | ||
|---|---|---|
| TNBC Tumors from European American Patients (n = 78) | ||
| Enriched upstream regulator | Activation z-score | P |
| ESR1 | 3.34 | 0.00000 |
| ETV3 | 2.24 | 0.01900 |
| BATF | 2.00 | 0.00350 |
| ETV5 | 2.00 | 0.01140 |
| JUN | 1.90 | 0.00003 |
| FOS | 1.89 | 0.00033 |
| MNT | 1.89 | 0.00070 |
| SREBF2 | 1.83 | 0.00320 |
| GATA3 | 1.62 | 0.01420 |
| SREBF1 | 1.38 | 0.00660 |
| ESR2 | 0.90 | 0.00155 |
| STAT3 | 0.87 | 0.00001 |
| CLOCK | 0.71 | 0.03700 |
| PRDM1 | 0.68 | 0.00000 |
| EGR2 | 0.67 | 0.00350 |
| JUNB | 0.56 | 0.02200 |
| CUX1 | 0.56 | 0.03600 |
| NR4A2 | 0.54 | 0.00097 |
| FOSL1 | 0.52 | 0.00260 |
| BACH2 | 0.39 | 0.01100 |
| EGR1 | 0.38 | 0.01260 |
| SRF | 0.11 | 0.01550 |
| TNBC Tumors from African American Patients (n = 34) | ||
| Enriched upstream regulator | Activation z-score | P |
| TCF3 | 2.53 | 0.00000 |
| MYF6 | 2.22 | 0.00686 |
| IRF9 | 2.19 | 0.02030 |
| REST | 2.19 | 0.00003 |
| POU2F2 | 2.12 | 0.00020 |
| POU4F1 | 2.00 | 0.02490 |
| BHLHE40 | 1.94 | 0.00214 |
| TBX21 | 1.83 | 0.00003 |
| PAX5 | 1.77 | 0.00001 |
| TCF4 | 1.70 | 0.00001 |
| KLF6 | 1.56 | 0.00220 |
| TFAP2A | 1.30 | 0.00400 |
| NR3C2 | 1.29 | 0.00487 |
| IRF8 | 0.89 | 0.00523 |
| EOMES | 0.89 | 0.00990 |
| TP63 | 0.68 | 0.00930 |
| TP53 | 0.61 | 0.00484 |
| HOXA10 | 0.58 | 0.00290 |
| SMAD3 | 0.56 | 0.00000 |
| MSC | 0.39 | 0.00000 |
| SP3 | 0.37 | 0.00170 |
| FOXA1 | 0.22 | 0.00003 |
| RARA | 0.11 | 0.03070 |
| FOXP3 | 0.05 | 0.00112 |
| CTCF | 0.05 | 0.00014 |
aTFs displayed that specifically overlapped with those identified by cell line ATAC analyses.