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Table 2 Selection of genes identified using CIA

From: Cross-platform comparison and visualisation of gene expression data using co-inertia analysis

Axis Cell lines Genes* Description Spotted cDNA Affymetrix
F1 (mesenchymal) All CNS, Renal cells and the breast cancer cell line BR-Hs578T COL1A1 Collagen marker - +
   COL4A1 Collagen marker + -
   COL4A2 Collagen marker - +
   TPM1 Muscle marker - +
   VIM Vimentin - +
   FN1 Fibronectin 1 + +
   TGF β Inducer of EMT - +
   CDH2 N-cadherin + -
   MT2A Metallothionein A2-associated with invasive breast cancer - +
F1 (epithelial) All colon cells and the breast cancer cells MCF-7 and TR7D CDH1 E-cadherin, primary epithelial marker + -
   SPINT2 Serine protease inhibitor, Kunitz type, 2 an inhibitor of hepatocyte growth factor + +
   KRT8 Keratin 8, epithelial marker + +
   KRT18 Keratin 18, epithelial marker - +
   KRT19 Keratin 19, epithelial marker - +
   DSP Desmoplakin I, epithelial marker + -
   S100A2 Loss of S100A2 early event in melanoma development - +
F1 (colon cell markers)   TACSTD1 Ep-Cam. Target antigen in colorectal carcinoma + +
   CDKN2A Target antigen in colorectal carcinoma + -
F1 (Leukaemia) All leukaemia cell lines ARHGDIB A lymphoid-specific guanosine diphosphate dissociation inhibitor + +
   LCP1 Lymphocyte cytosolic protein 1, L-plastin + -
   IFITM1 An interferon induced transmembrane protein - +
F2 (Melanoma) All melanoma cells and the breast cancer cells BR_MDA and BR_MDAMB435 MITF Microphthalamia-associated transcription factor - +
   TYR Tyrosinase - +
   DCT Dopachrome tautomerase - +
   TYRP1 Tyrosinase-related protein 1 - +
   RAB7 Ras-associated protein 7 - +
   MIA Melanoma inhibitory activity - +
   MCAM MUC18, melanoma cell adhesion molecule MCAM + -
   MAGE 3 Melanoma-associated antigen 3 - +
   MAGE 12 Melanoma-associated antigen 12 - +
   GPNMB Glycomembrane protein nmb - +
   TIMP2 Tissue inhibitor of metalloproteinase 2 - +
   TIMP3 Tissue inhibitor of metalloproteinase 3 + -
  1. Genes identified on the first (F1) and second (F2) axes, where + or - indicated whether a gene was detected or not detected within the top 30 genes at the ends of each of these axes in CIA of Affymetrix and spotted cDNA array gene expression profiles of the NCI60 cell lines. These genes are graphically presented in Figure 4 and further details on these genes are available in the Results section. *Official gene symbol names are used for each gene.