Table 1. Summary characteristics and ranking of 42 melanoma cell lines based on average Pearson’s correlation of their expression profiles with single malignant melanoma cells.
| Mean correlation to | |||||||
|---|---|---|---|---|---|---|---|
| all malignant tumour cells | the top MITF program enriched malignant cells | the top AXL program enriched malignant cells | Cell line MITF gene set enrichment | Cell line AXL gene set enrichment | Predominant MITF/AXL cluster | PubMed Citations, n | |
| COLO 849 | 0.542 | 0.530 | 0.508 | 2.96 | -0.39 | MITF | 0 |
| SK-MEL-30 | 0.535 | 0.603 | 0.458 | 1.78 | -0.28 | MITF | 15 |
| UACC-257 | 0.531 | 0.601 | 0.451 | 2.43 | -0.80 | MITF | 18 |
| A375 | 0.529 | 0.510 | 0.512 | -3.46 | 1.32 | AXL | 1663 |
| 537 MEL | 0.528 | 0.521 | 0.488 | 0.18 | 1.54 | Intermediate | 4 |
| IPC-298 | 0.523 | 0.510 | 0.488 | 0.25 | 0.93 | Intermediate | 6 |
| LOX-IMVI | 0.523 | 0.523 | 0.490 | -3.53 | 1.96 | AXL | 39 |
| COLO 792 | 0.521 | 0.577 | 0.447 | 2.78 | -1.99 | MITF | 0 |
| SK-MEL-28 | 0.519 | 0.578 | 0.459 | 2.17 | -0.64 | MITF | 451 |
| HMY-1 | 0.516 | 0.563 | 0.466 | 2.07 | -1.91 | MITF | 4 |
| SK-MEL-2 | 0.515 | 0.539 | 0.475 | 2.69 | -1.48 | MITF | 250 |
| SK-MEL-31 | 0.514 | 0.429 | 0.524 | -0.50 | 4.30 | Intermediate | 4 |
| SK-MEL-24 | 0.514 | 0.437 | 0.514 | 0.46 | 3.20 | Intermediate | 32 |
| MeWo | 0.513 | 0.565 | 0.454 | 1.81 | 1.34 | MITF | 322 |
| HT-144 | 0.511 | 0.521 | 0.476 | 2.00 | 0.51 | MITF | 55 |
| G-361 | 0.510 | 0.569 | 0.459 | 2.13 | -2.76 | MITF | 287 |
| 624-mel | 0.510 | 0.596 | 0.443 | 1.15 | 0.17 | MITF | 9 |
| MEL-HO | 0.507 | 0.575 | 0.415 | 1.75 | -1.55 | MITF | 11 |
| Hs 936.T | 0.505 | 0.554 | 0.456 | 2.34 | -2.22 | MITF | 0 |
| SK-MEL-5 | 0.505 | 0.579 | 0.441 | 1.98 | -2.45 | MITF | 112 |
| IGR-37 | 0.503 | 0.566 | 0.444 | 1.87 | -2.02 | MITF | 12 |
| MDA-MB-435 | 0.503 | 0.474 | 0.484 | -3.33 | 2.09 | AXL | 1239 |
| 928 mel | 0.502 | 0.570 | 0.439 | 2.75 | -2.84 | MITF | 8 |
| COLO 794 | 0.501 | 0.457 | 0.489 | -0.84 | 3.10 | Intermediate | 0 |
| RPMI-7951 | 0.500 | 0.471 | 0.474 | -4.46 | 3.22 | AXL | 45 |
| COLO 679 | 0.500 | 0.488 | 0.500 | 1.14 | -1.65 | MITF | 5 |
| A2058 | 0.499 | 0.509 | 0.458 | -1.09 | -1.75 | MITF | 358 |
| C32 | 0.497 | 0.434 | 0.504 | -0.88 | 2.33 | Intermediate | 157 |
| UCSD-242l | 0.488 | 0.455 | 0.467 | -1.01 | 3.01 | Intermediate | 0 |
| SK23 | 0.484 | 0.537 | 0.441 | 1.88 | -0.73 | MITF | 12 |
| SK-MEL-1 | 0.483 | 0.473 | 0.452 | 1.84 | -1.77 | MITF | 46 |
| COLO 783 | 0.482 | 0.453 | 0.454 | 1.04 | 2.13 | Intermediate | 0 |
| 888 mel | 0.473 | 0.540 | 0.418 | 2.15 | -2.60 | MITF | 14 |
| Hs 294.T | 0.468 | 0.440 | 0.446 | -4.33 | 3.96 | AXL | 74 |
| SK-MEL-3 | 0.465 | 0.532 | 0.410 | 2.37 | -0.44 | MITF | 43 |
| Hs 940.T | 0.460 | 0.456 | 0.431 | -3.32 | 2.35 | AXL | 0 |
| WM-115 | 0.449 | 0.393 | 0.453 | -1.51 | 3.63 | Intermediate | 64 |
| Hs 695.T | 0.443 | 0.389 | 0.441 | -1.58 | 2.69 | Intermediate | 0 |
| DEOC-1 | 0.436 | 0.483 | 0.383 | 1.71 | 1.67 | MITF | 1 |
| Hs 895.T | 0.416 | 0.370 | 0.406 | -3.18 | 3.34 | AXL | 0 |
| Hs 852.T | 0.285 | 0.295 | 0.248 | -2.61 | 0.46 | AXL | 0 |
| Hs 839.T | 0.216 | 0.189 | 0.224 | -2.70 | 2.36 | AXL | 1 |
All genes were used to compute the Pearson’s correlation of all the cell line-malignant cell pairs. The cell lines were ranked based on their average correlation indicated malignant cells (n = 1256). MITF and AXL program enriched cells represent the cells with the highest and lowest 400 MITF/AXL enriched cells, respectively. MITF or AXL gene set enrichment is indicated based on GAGE analyses. MITF, AXL or intermediate clusters were structured based on Gaussian kernels.