Table 4.
BC Cell Line Names and Types That Were Used for Standard K-Means Clustering
| BC Cell Line Subtype | FOXQ1 Relative Expression | FOXQ1 Relative CNV | Unsupervised K-Means Clusters | Supervised K-Means Clusters |
|---|---|---|---|---|
| TNBC | ||||
| CAL-148 | 0.046847 | −0.1 | ||
| DU4475 | 0.071856 | −0.1 | ||
| CAL-51 | 0.047552 | 0 | ||
| HCC1395 | 0.093519 | 0.41 | ||
| BT-549 | 0.036633 | 0.04 | ||
| HCC1806 | 1 | 0.49 | ||
| MDA-MB-231 | 0.71962 | 0.41 | ||
| CAL-120 | 0.550194 | 0.29 | ||
| CAL-851 | 0.63156 | 0.28 | ||
| HDQ-P1 | 0.797992 | 0.20 | ||
| HCC38 | 0.344311 | 0.51 | ||
| Hs 578T | 0.373547 | 0.24 | ||
| HCC1187 | 0.327932 | 0.3 | ||
| HCC1143 | 0.686685 | −0.15 | ||
| HCC70 | 0.713632 | −0.09 | ||
| HCC1937 | 0.775097 | −0.48 | ||
| MDA-MB-436 | 0.551427 | −0.33 | ||
| MDA-MB-157 | 0.037161 | 0.02 | ||
| HCC2157 | 0.058471 | −0.82 | ||
| BT-20 | 0.057591 | −0.67 | ||
| Luminal | ||||
| CAMA-1 | 0.031349 | 0.08 | ||
| MDA-MB-415 | 0.070447 | −0.16 | ||
| EFM-192A | 0.034519 | 0.18 | ||
| BT-483 | 0.068158 | −0.05 | ||
| KPL-1 | 0.095104 | −0.15 | ||
| MCF-7 | 0.024833 | 0 | ||
| MDA-MB-175 | 0.435717 | −0.24 | ||
| MDA-MB-134 | 0 | −0.01 | ||
| HCC1428 | 0.054773 | −0.48 | ||
| HER2 | ||||
| MDA-MB-453 | 0.023248 | −0.07 | ||
| HCC1569 | 0.016555 | −0.08 | ||
| HCC2218 | 0.027474 | −0.03 | ||
| HCC202 | 0.012328 | 0.14 | ||
| HCC1954 | 0.441881 | 0.09 | ||
| JIMT-1 | 0.447693 | −0.22 | ||
| AU565 | 0.054773 | −0.54 | ||
Notes: Cell line types were sorted as described in.46,47 The mRNA expression and CNV of FOXQ1 in 36 BC cell lines were obtained from CCLE online database.45 Cell lines with no defined subtypes were not considered for consistency. Four clusters were used for unsupervised K-means clustering, while 3 clusters were used for supervised clustering. For supervised and unsupervised clustering, cell lines within each column that have the same color are grouped together. These clusters and data are plotted in Figure 5.