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Table 3 Genes differentially expressed between tumor versus normal cells by both rank products and pairwise analysis

From: Novel markers for differentiation of lobular and ductal invasive breast carcinomas by laser microdissection and microarray analysis

Probe Set1 Gene Symbol Gene Title Fold-change
    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
  1. Tduc – ductal tumor; Tlob – lobular tumor; D – normal ductal cells; L – normal lobular cells; n – not differentially expressed among top 20 genes.
  2. 1Affymetrix probe set number; If there was more than one probe set for the particular gene found among top 20 changed genes (according to the fold change), the probe set with the highest fold change is used and number of other probe set is indicated.