Table 1.
Genes with highest frequencies in 500 signatures
| Gene title | Gene symbol | Frequency |
| Top 20 core genes from ER-positive tumors | ||
| KIAA0241 protein | KIAA0241 | 321 |
| CD44 antigen (homing function and Indian blood group system) | CD44 | 286 |
| ATP-binding cassette, sub-family C (CFTR/MRP), member 5 | ABCC5 | 251 |
| serine/threonine kinase 6 | STK6 | 245 |
| cytochrome c, somatic | CYCS | 235 |
| KIAA0406 gene product | KIA0406 | 212 |
| uridine-cytidine kinase 1-like 1 | UCKL1 | 201 |
| zinc finger, CCHC domain containing 8 | ZCCHC8 | 188 |
| Rac GTPase activating protein 1 | RACGAP1 | 186 |
| staufen, RNA binding protein (Drosophila) | STAU | 176 |
| lactamase, beta 2 | LACTB2 | 175 |
| eukaryotic translation elongation factor 1 alpha 2 | EEF1A2 | 172 |
| RAE1 RNA export 1 homolog (S. pombe) | RAE1 | 153 |
| tuftelin 1 | TUFT1 | 150 |
| zinc finger protein 36, C3H type-like 2 | ZFP36L2 | 150 |
| origin recognition complex, subunit 6 homolog-like (yeast) | ORC6L | 143 |
| zinc finger protein 623 | ZNF623 | 140 |
| extra spindle poles like 1 | ESPL1 | 139 |
| transcription elongation factor B (SIII), polypeptide 1 | TCEB1 | 138 |
| ribosomal protein S6 kinase, 70 kDa, polypeptide 1 | RPS6KB1 | 127 |
| Top 20 core genes from ER-negative tumors | ||
| zinc finger protein, multitype 2 | ZFPM2 | 445 |
| ribosomal protein L26-like 1 | RPL26L1 | 372 |
| hypothetical protein FLJ14346 | FLJ14346 | 372 |
| mitogen-activated protein kinase-activated protein kinase 2 | MAPKAPK2 | 347 |
| collagen, type II, alpha 1 | COL2A1 | 340 |
| muscleblind-like 2 (Drosophila) | MBNL2 | 320 |
| G protein-coupled receptor 124 | GPR124 | 314 |
| splicing factor, arginine/serine-rich 11 | SFRS11 | 300 |
| heterogeneous nuclear ribonucleoprotein A1 | HNRPA1 | 297 |
| CDC42 binding protein kinase alpha (DMPK-like) | CDC42BPA | 296 |
| regulator of G-protein signalling 4 | RGS4 | 276 |
| transient receptor potential cation channel, subfamily C, member 1 | TRPC1 | 265 |
| transcription factor 8 (represses interleukin 2 expression) | TCF8 | 263 |
| chromosome 6 open reading frame 210 | C6orf210 | 262 |
| dynamin 3 | DNM3 | 260 |
| centrosome protein Cep63 | Cep63 | 251 |
| tumor necrosis factor (ligand) superfamily, member 13 | TNFSF13 | 251 |
| dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis) | DACT1 | 248 |
| heterogeneous nuclear ribonucleoprotein A1 | HNRPA1 | 245 |
| reversion-inducing-cysteine-rich protein with kazal motifs | RECK | 243 |
The top 20 genes are ranked by their frequency in the 500 signatures of 100 genes for ER-positive and ER-negative tumors (for details see Figure 1).