Table 3.
Comparison of RNA-Seq and immunohistochemistry data.
| Gene | Protein | MCF10A | MCF7 | T47D | MDA231 | MDA436 | HCC1937 | SUM149 | SUM1315 | SL | SB | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RNA-Seq | ESR1 | ERalpha | 0 | 1.05 | 0.88 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| IHC | ER | - | + (90%) | + (50%) | - | - | - | - | - | - | - | |
| RNA-Seq | PGR | PR | 0 | 0 | 0.45 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| IHC | PR | - | + (40%) | + (80%) | - | - | - | - | - | - | - | |
| RNA-Seq | ERBB2 | HER2 | 0.40 | 1.31 | 0.90 | 0.46 | 0 | 0.43 | 0.36 | 0 | 0 | 0 |
| IHC | HER2 | - | - | - | - | - | - | - | - | - | - | |
| RNA-Seq | KRT5 | CK5 | 148.0 | 0 | 0 | 0 | 0 | 11.7 | 6.3 | 0 | 0 | 0 |
| KRT6A | CK6 | 102.9 | 0 | 0 | 0 | 0 | 0.8 | 8.2 | 0 | 0 | 0 | |
| KRT6B | CK6 | 6.8 | 0 | 0 | 0 | 0 | 0 | 5.1 | 0 | 0 | 0 | |
| KRT6C | CK6 | 3.7 | 0 | 0 | 0 | 0 | 0.3 | 2.4 | 0 | 0 | 0 | |
| IHC | CK5/6 | + (90%) | - | - | - | - | + (25%) | + (25%) | - | - | - | |
| RNA-Seq | KRT14 | CK14 | 76.1 | 0 | 0 | 0.3 | 0 | 5.5 | 0.4 | 0 | 0 | 0 |
| IHC | CK14 | + (80%) | - | - | - | - | + (20%) | + (<1%) | - | - | - | |
| RNA-Seq | EGFR | EGFR | 0.90 | 0 | 0 | 0.88 | 0.82 | 0.50 | 1.22 | 0.44 | 0.51 | 0.62 |
| IHC | EGFR | + (100%) | - | + (40%) | + (100%) | + (90%) | + (100%) | + (100%) | + (90%) | + (60%) | + (80%) |
RNA-Seq results are presented as RPKM values. Results of immunohistochemistry are presented as negative (-) or positive (+), specifying the percentage of labeled cells.
IHC: immunohistochemistry; ER: estrogen receptor; PR: progesteron receptor; CK: cytokeratin.