Table 2.
Summary of the 43 individuals identified as outliers by robust sparse logistic regression regarding ER, PR, and HER2 gene expression and corresponding clinical label (within parentheses).
| Genes |
||||||||
|---|---|---|---|---|---|---|---|---|
| ER | PR | HER2 |
||||||
| FPKM (clinical) | FPKM (clinical) | FPKM | (clinical) |
|||||
| Individual | level IHC | status IHC | status FISH | Clinical type | ||||
| 1 | TCGA-AR-A1AO | 1.47(+) | 1.13(−) | 14.89 | (−) | (−) | non-TNBC | |
| 2 | TCGA-BH-A6R9 | 0.59(−) | 0.25(+) | 8.18 | (−) | non-TNBC | ||
| 3 | TCGA-AC-A62X | 0.19(+) | 0.02(−) | 28.53 | non-TNBC | |||
| 4 | TCGA-A2-A0YJ | 0.09(+) | 0.03(−) | 240.24 | (−) | (−) | non-TNBC | |
| 5 | TCGA-LL-A5YP | 0.16(+) | 0.05(−) | 15.10 | (−) | (−) | (+) | non-TNBC |
| 6 | TCGA-A7-A13D | 0.52(−) | 0.81(+) | 42.28 | (Ind) | (Equiv) | (−) | non-TNBC |
| 7 | TCGA-E2-A1II | 0.14(−) | 0.19(+) | 10.73 | (−) | (−) | non-TNBC | |
| 8 | TCGA-AR-A1AH | 0.03(+) | 0.03(−) | 34.12 | (−) | non-TNBC | ||
| 9 | TCGA-BH-A0DL | 6.99(+) | 0.04(−) | 9.92 | (−) | non-TNBC | ||
| 10 | TCGA-E2-A14Y | 0.67(+) | 0.03(+) | 487.90 | (Ind) | (Equiv) | (+) | non-TNBC |
| 11 | TCGA-AO-A0JL | 0.63(−) | 0.08(−) | 63.60 | (−) | (−) | (+) | non-TNBC |
| 12 | TCGA-AN-A0FL | 0.09(−) | 1.07(−) | 15.07 | (−) | (+) | non-TNBC | |
| 13 | TCGA-AO-A1KO | 10.78(+) | 9.12(+) | 14.91 | (−) | (−) | non-TNBC | |
| 14 | TCGA-AN-A0FX | 1.13(−) | 0.64(−) | 24.02 | (−) | (+) | non-TNBC | |
| 15 | TCGA-A1-A0SB | 3.16(+) | 0.03(−) | 32.35 | (−) | non-TNBC | ||
| 16 | TCGA-D8-A1JM | 5.01(+) | 0.01(−) | 21.85 | (−) | (−) | non-TNBC | |
| 17 | TCGA-E9-A1NC | 0.11(−) | 0.08(+) | 15.91 | (+) | non-TNBC | ||
| 18 | TCGA-A2-A25F | 0.62(−) | 0.23(+) | 5.19 | (−) | non-TNBC | ||
| 19 | TCGA-A2-A1G1 | 0.53(−) | 0.17(−) | 819.76 | (Ind) | (Equiv) | (+) | non-TNBC |
| 20 | TCGA-LL-A6FR | 0.33(−) | 0.04(+) | 32.13 | (Ind) | (Equiv) | (+) | non-TNBC |
| 21 | TCGA-A2-A3Y0 | 2.18(+) | 0.03(−) | 11.34 | (−) | (−) | non-TNBC | |
| 22 | TCGA-B6-A0IJ | 1.18(+) | 0.46(+) | 11.12 | non-TNBC | |||
| 23 | TCGA-AR-A0TP | 0.04(+) | 0.03(−) | 13.39 | (−) | non-TNBC | ||
| 24 | TCGA-S3-AA0Z | 16.67(+) | 0.07(+) | 33.07 | (−) | (Equiv) | (−) | non-TNBC |
| 25 | TCGA-A2-A4S1 | 0.29(+) | 0.01(−) | 0.61 | (−) | non-TNBC | ||
| 26 | TCGA-A7-A13E | 0.82(+) | 0.06(−) | 46.08 | (Ind) | (Equiv) | (−) | non-TNBC |
| 27 | TCGA-D8-A1JK | 0.40(−) | 0.72(+) | 22.19 | (−) | (−) | non-TNBC | |
| 28 | TCGA-E9-A1ND | 1.44(−) | 0.05(−) | 13.05 | (+) | non-TNBC | ||
| 29 | TCGA-JL-A3YW | 0.35(+) | 0.09(+) | 31.47 | (−) | (+) | non-TNBC | |
| 30 | TCGA-AN-A0FJ | 0.08(+) | 0.04(−) | 14.28 | (−) | (+) | non-TNBC | |
| 31 | TCGA-D8-A1XW | 0.32(−) | 0.11(+) | 21.03 | (−) | (−) | non-TNBC | |
| 32 | TCGA-UU-A93S | 0.30(−) | 0.12(−) | 1668.35 | (+) | (+) | non-TNBC | |
| 33 | TCGA-OL-A5S0 | 0.09(+) | 0.06(−) | 31.92 | (+) | non-TNBC | ||
| 34 | TCGA-E9-A22G | 0.44(−) | 0.02(−) | 15.32 | (+) | non-TNBC | ||
| 35 | TCGA-AR-A24Q | 1.00(+) | 0.36(−) | 20.67 | (−) | non-TNBC | ||
| 36 | TCGA-E2-A1B0 | 0.14(−) | 0.26(−) | 563.81 | (+) | (+) | non-TNBC | |
| 37 | TCGA-AR-A251 | 1.57(+) | 0.10(−) | 14.02 | (Ind) | (Equiv) | (−) | non-TNBC |
| 38 | TCGA-A2-A4RX | 0.68(+) | 0.93(+) | 26.64 | (−) | (−) | non-TNBC | |
| 39 | TCGA-AR-A1AJ | 1.47(+) | 0.07(−) | 9.74 | (−) | non-TNBC | ||
| 40 | TCGA-A2-A04U | 0.02(−) | 0.02(−) | 9.64 | (−) | (−) | (+) | non-TNBC |
| 41 | TCGA-BH-A5IZ | 5.12(+) | 0.03(−) | 28.08 | (−) | (−) | non-TNBC | |
| 42 | TCGA-D8-A13Y | 15.48(+) | 4.17(+) | 4.83 | (−) | (−) | non-TNBC | |
| 43 | TCGA-LL-A8F5 | 1.08(+) | 0.04(−) | 11.86 | (−) | (−) | non-TNBC | |
Note: Individuals highlighted in bold correspond to individuals previously identified as suspicious as described in the Data description section. FPKM: fragments per kilobase million; Ind: indeterminate; Equiv: equivocal; ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2.