Table 2. Genes up-regulated or down-regulated in Amela tumors involved in EMT.
| Gene symbol | Gene name | (b)Log2 ratio Amela/Mela | (c)Log2 ratio Amela/Lines |
| (a)Cell adhesion/ECM matrix/Cytoskeleton | |||
| Itgbl1 | Integrin beta like 1 | 2.18 | 0.20 |
| Lamb1–1 | Laminin beta 1, subunit 1 | 1.47 | −0.76 |
| Sdc2 | Syndecan-1 | 1.36 | 0.36 |
| Cdh2 | N-cadherin | 1.25 | −0.33 |
| Col4a1 | Collagen, type IV, alpha 1 | 0.99* | 0.87 |
| Col11a1 | Collagen, type XI, alpha 1 | 0.81* | −0.54 |
| Itgav | Integrin alpha 5 | 0.62* | −0.30 |
| Col6a1 | Collagen, type VI, alpha 1 | 0.57* | 0.96 |
| Itga3 | Integrin alpha 3 | 0.46* | −1.90 |
| (a)Proteases . Protease Iinhibitors | |||
| Mmp10 | Metallopeptidase 10 | 2.67 | 1.26 |
| Pcolce | Procollagen C-endopeptidase enhancer protein | 1.03 | −0.93 |
| Mmp19 | Metallopeptidase 19 | 0.92* | 0.20 |
| Serpinb9 | Serine peptidase inhibitor, Clade B, member9 | 0.72* | 0.75 |
| (a)PDGF/PDGF receptor pathway | |||
| Ccl2 | Chemokine CC motif ligand 2 | 2.23 | −2.46 |
| Pdgfc | Platelet dervied growth factor, C polypeptide | 1.59 | −0.31 |
| Cmkor1 | Chemokine CXC motif receptor 7 (CXCR7) | 1.46 | −0.52 |
| Pdgfa | Platelet dervied growth factor, alpha | 0.67 | 0.39 |
| Pdgfd | Platelet dervied growth factor, D polypeptide | 0.47 | 0.26 |
| (a)Hypoxia | |||
| Upp1 | Uridine phosphorylase | 1.74 | −0.75 |
| Il11 | Interleukin 11 | 1.69 | −0.97 |
| Hif1a | hypoxia inducible factor 1, alpha subunit | 0.59* | −1.46 |
| (a)Transcription factors | |||
| Hmga2 | high mobility group alpha 2 | 3.71 | −1.05 |
| Twist1 | Twist homolog 1 (Drosophila) | 2.07 | −0.78 |
| Foxc2 | Forkhead box c2 | 1.36 | −0.40 |
| Snai1 | Snail homolog 1 (Drosophila)/Snail1 | 1.16 | −0.07 |
| (d) Down-regulated in Amela | |||
| Cdh1 | E-Cadherin | −3.62 | 2.28 |
| Id2 | Inhibitor of DNA binding 2 | −0.83* | 0.6 |
(a)
Genes known to be involved in EMT that show higher expression in Amela versus Mela primary tumors and are expressed at similar level in Amela primary tumors and Amela lines in culture.
(b)
Ratio of gene expression as log2 primary Amela/primary Mela > 1 with p values < 0.05;
*
Ratio of gene expression as log2 primary Amela/primary Mela between 0 and 1 with p values < 0.05;
(c)
Ratio of gene expression as Log2 (primary Amela-/cultured Amela line) < 1 and/or with p value > 0.05 (ns). Log2 (primary Amela /cultured Amela line) < - 1 corresponds to higher expression in cultured Amela line than in primary Amela.
(d)
Genes known to be involved in EMT that show lower expression in primary Amela versus Mela tumors.