Table 3. Representative TGFβ Related Genes expressed in Amela tumors and cultured cell lines.
| TGFβ related genes | ||||
| (a)Gene symbol | Gene name | (b)log2 ratioAmela/Mela | (c)log2 ratioAmela /Lines | (d)References |
| Igfbp3 | Insulin-like growth factor binding protein 3 | 3.15 | 0.64 | [1] |
| Cspg2 | Versican | 2.55 | 0.04 | [2]–[4] |
| Itgbl1 | Integrin beta-like 1 | 2.18 | 0.20 | [4] |
| Cald1 | Caldesmon 1 | 1.93 | −0.08 | [5]–[7] |
| Ltbp1 | Latent transforming growth factor beta binding protein 1 | 1.78 | −0.66 | [8] |
| Nid1 | Nidogen | 1.72 | 0.66 | [9] |
| Igfbp4 | Insulin-like growth factor binding protein 4 | 1.60 | 1.64 | [10] |
| Lamb1–1 | Laminin B1 subunit 1 | 1.47 | −0.76 | [4], [7], [11]–[12] |
| Cmkor1 | Chemokine CXC motif receptor 7 (RDC1, CXCR7) | 1.46 | −0.52 | [2], [6], [12]–[14] |
| Fhl2 | Four and a half LIM domains 2 | 1.43 | −0.40 | [2], [6]–[7], [12]–[13] |
| Lrp1 | Low density lipoprotein receptor-related protein 1 | 1.40 | 0.88 | [15] |
| Plat | Plasminogen activator, tissue | 1.40 | 0.99 | [16] |
| Bmp1 | Bone morphogenetic protein 1 | 1.30 | 0.54 | [6]–[7], [12] |
| Smad3 | MAD homolog 3 (Drosophila) | 1.19 | −0.23 | [17] |
| Slc29a1 | Solute carrier family 29 (nucleoside transporters), member 1 | 1.18 | 1.00 | [5], [7], [12] |
| Cdh6 | Cadherin 6 | 1.18 | 0.28 | |
| Rdh10 | Retinol dehydrogenase 10 (all-trans) | 1.11 | 0.29 | [6]–[7], [13] |
| Col4a1 | Collagen type IV, alpha 1 | 0.99* | 0.87 | [7], [11]–[13] |
| Wnt2 | Wingless-related MMTV integration site 2 | 0.97* | 0.48 | [18] |
| Tgfbr2 | Transforming growth factor receptor 2 | 0.96* | 0.01 | [19] |
| Marcksl1 | MARCKS-like 1 | 0.94* | 0.88 | [20] |
| Rhoq | Ras homolog gene family, member Q | 0.90* | 0.37 | [20] |
| Ext1 | Extososes multiple 1 | 0.85* | 0.43 | [2], [6]–[7] |
| Ier3 | Immediate early response 3 | 0.84* | −0.43 | [5], [7], [12]–[13] |
| Tgfb3 | Transforming growth factor 3 | 0.82* | 0.23 | [19] |
| Pdgfa | Platelet derived growth factor, alpha | 0.67* | 0.39 | [2], [5]–[7], [21] |
| Col6a1 | Collagen type VI, alpha 1 | 0.57* | 0.96 | [4], [7], [22] |
| Itga3 | Integrin alpha 3 | 0.46* | −1.90 | [4], [7], [23] |
| Cd44 | CD44 antigen | 0.41* | −1.47 | [24] |
| Skil | SKI-like | 0.40* | 0.49 | [2], [7], [13] |
| Igf2r | Insulin-like growth factor 2 receptor | 0.38* | 0.10 | |
| Tgfbr3 | Transforming growth factor receptor 3 | 0.20* | −0.23 | [19] |
(a)
Genes known to be TGFβ responsive that show higher expression in Amela versus Mela primary tumors and are expressed at similar level in Amela primary tumors and in 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 lines than in primary tumor.
(d)
Numbered references can be found in Text S1.