Table 3 Genes differentially expressed between tumor versus normal cells by both rank products and pairwise analysis
Probe Set1 | Gene Symbol | Gene Title | Fold-change | |||
|---|---|---|---|---|---|---|
| Â | Â | Â | Tduc | Tlob | ||
Lobular carcinoma vs normal cells (↑ – upregulated in Tlob, ↓ – downregulated in Tlob) | L | D | L | D | ||
Extracellular matrix-receptor interaction and focal adhesion (epithelial-mesenchymal transition) | ||||||
227314_at | ITGA2↓ | Integrin, alpha 2 | n | n | -4.7 | -6.2 |
201438_at | COL6A3↑ | Collagen, type VI, alpha 3 | n | n | 4.5 | 7.7 |
203083_at | THBS2↑ | Thrombospondin 2 | n | n | 6.5 | 6.5 |
205713_s_at | COMP↑ | Cartilage oligomeric matrix protein | n | n | 6.7 | 8.1 |
226237_at | COL8A1↑ | Collagen, type VIII, alpha 1 | n | n | 8.4 | 5.9 |
225681_at | CTHRC1↑ | Collagen triple helix repeat containing 1 | n | n | 18.5 | 48.4 |
219087_at | ASPN↑ | Asporin | n | n | 23.3 | 22.1 |
WNT signalling | ||||||
223121_s_at 223122_s_at | SFRP2↑ | Secreted frizzled-related protein 2 | n | n | 5.8 3.9 | 7.4 7.1 |
229802_at | WISP1↑ | WNT1 inducible signaling pathway protein 1 | n | n | 9.1 | 12.4 |
Actin, calcium and metal ion binding | ||||||
204455_at | DST↓ | Dystonin | n | n | -22.2 | -18.3 |
214087_s_at | MYBPC1↓ | Myosin binding protein C, slow type | n | n | -10.1 | -12.2 |
209301_at | CA2↓ | Carbonic anhydrase II | n | n | -9.2 | -8.7 |
206509_at | PIP↓ | Prolactin-induced protein | n | n | -7.0 | -6.3 |
201131_s_at | CDH1↓ | Cadherin 1, type 1, E-cadherin | n | n | -6.2 | -7.2 |
226777_at | ADAM12↑ | ADAM metallopeptidase domain 12 | n | n | 5.7 | 5.3 |
213905_x_at | BGN/SDCCAG33↑ | Biglycan/serologically defined colon cancer antigen 33 | n | n | 8.3 | 7.2 |
Other | ||||||
227742_at | CLIC6↓ | Chloride intracellular channel 6 | n | n | -9.3 | -8.2 |
225817_at | CGNL1↓ | Cingulin-like 1 | n | n | -5.9 | -7.8 |
219850_s_at | EHF↓ | Ets homologous factor | n | n | -4.1 | -6.3 |
213975_s_at | LYZ/ILRB1↑ | Lysozyme | n | n | 10.8 | 7.3 |
Ductal carcinoma vs normal cells (↓ – upregulated in Tduc, ↓ – downregulated in Tduc) | ||||||
Regulation of transcription | ||||||
202672_s_at | ATF3↓ | Activating transcription factor 3 | -4.5 | -7.7 | n | n |
226147_s_at | PIGR↓ | Polymeric immunoglobulin receptor | -4.8 | -10 | n | n |
Cytokine and growth factor activity | ||||||
209466_x_at 211737_x_at | PTN↓ | Pleiotrophin | -5.8 -7.1 | -8.3 -12.5 | n | n |
823_at | CX3CL1↓ | Chemokine (C-X3-C motif) ligand 1 | -3.6 | -8.3 | n | n |
Ion transport and metabolism | ||||||
203296_s_at | ATP1A2↓ | ATPase, Na+/K+ transporting, alpha 2 | -8.2 | -9.6 | n | n |
204259_at | MMP7↓ | Matrix metallopeptidase 7 | -4.5 | -7.2 | n | n |
212353_at | SULF1↓ | Sulfatase 1 | 4.6 | 4.0 | n | n |
Other | ||||||
1553602_at | LOC118430↓ | Small breast epithelial mucin | -7.1 | -10.4 | n | n |
223623_at | ECRG4↓ | Esophageal cancer related gene 4 protein | -6.6 | -5.6 | n | n |
206548_at | FLJ23556↓ | Hypothetical protein FLJ23556 | -6.3 | -11.2 | n | n |
218585_s_at | DTL↑ | Denticleless homolog (Drosophila) | 3.6 | 4.8 | n | n |
Tumor vs normal cells (↑ – upregulated in tumor, ↓ – downregulated in tumor) | ||||||
Extracellular matrix-receptor interaction and focal adhesion (epithelial-mesenchymal transition) | ||||||
224823_at | MYLK↓ | Myosin, light polypeptide kinase | -3.5 | -3.4 | -5.9 | -5.4 |
204620_s_at 221731_x_at | CSPG2↑ | Chondroitin sulfate proteoglycan 2 (versican) | 3.0 3.5 | 4.9 5.3 | 4.5 4.0 | 5.8 6.1 |
221729_at | COL5A2↑ | Collagen, type V, alpha 2 | 3.5 | 4.4 | 9.3 | 11.3 |
211161_s_at | COL3A1↑ | Collagen, type III, alpha 1 | 4.1 | 3.3 | 9.8 | 14.9 |
212464_s_at | FN1↑ | Fibronectin 1 | 5.2 | 5.0 | 8.0 | 10.5 |
202311_s_at 202310_s_at | COL1A1↑ | Collagen, type I, alpha 1 | 5.6 5.1 | 6.0 5.1 | 12.7 10.4 | 13.0 10.8 |
37892_at | COL11A1↑ | Collagen, type XI, alpha 1 | 6.7 | 7.8 | 6.6 | 5.9 |
202404_s_at | COL1A2↑ | Collagen, type I, alpha 2 | 6.8 | 10.1 | 30.5 | 18.3 |
Ion and electron transport | ||||||
205044_at | GABRP↓ | Gamma-aminobutyric acid (GABA) A receptor, pi | -4.2 | -8.7 | -6.2 | -8.6 |
220230_s_at | CYB5R2↓ | Cytochrome b5 reductase 2 | -3.6 | -3.8 | -4.3 | -4.2 |
Regulation of transcription | ||||||
220625_s_at | ELF5↓ | E74-like factor 5 (ets domain transcription factor) | -4.0 | -4.8 | -5.9 | -8.4 |
209292_at | ID4↓ | Inhibitor of DNA binding 4 | -2.9 | -5.1 | -10.8 | -4.5 |
Actin and actin-binding proteins | ||||||
203951_at | CNN1↓ | Calponin 1, basic, smooth muscle | -6.7 | -6.6 | -6.9 | -7.3 |
243140_at | ACTA2↓ | Actin, alpha 2, smooth muscle, aorta | -4.0 | -4.1 | -8.7 | -4.0 |
WNT signaling | ||||||
202037_s_at | SFRP1↓ | Secreted frizzled-related protein 1 | -7.1 | -8.8 | -8.5 | -7.3 |
Intermediate filament proteins | ||||||
209351_at | KRT14↓ | Keratin 14 | -22.9 | -31.0 | -21.9 | -24.0 |
205157_s_at | KRT17↓ | Keratin 17 | -17.7 | -21.4 | -9.9 | -12.6 |
212730_at | DMN↓ | Desmuslin | -10.0 | -10.4 | -7.2 | -7.5 |
201820_at | KRT5↓ | Keratin 5 | -8.9 | -12.7 | -11.3 | -12.1 |
Other | ||||||
229947_at | PI15↓ | Peptidase inhibitor 15 | -6.5 | -7.5 | -18.5 | -15.0 |
205380_at | PDZK1↓ | PDZ domain containing 1 | -4.5 | -5.8 | -4.2 | -6.4 |
213909_at | LRRC15↑ | Leucine rich repeat containing 15 | 6.2 | 5.7 | 7.3 | 11.8 |