Table 2.
First 50 Genes with Highest Differential Expression in DFSP According to SAM Analysis
| Gene symbol | Gene name | UniGene # | GenBank # | SAM score(d) |
|---|---|---|---|---|
| ESTs | Hs.32345 | AI668612 | 11.1886 | |
| EGR2 | Early growth response 2 | Hs.1395 | AA446027 | 9.893322 |
| PLA2R1 | Phospholipase A2 receptor 1, 180 kD | Hs.171945 | W04525 | 9.403624 |
| PCDH18 | Protocadherin 18 | Hs.97266 | AA704401 | 9.161416 |
| ESTs | ESTs | Hs.192262 | AI192496 | 8.982065 |
| LOC51136 | LOC51136 PTD016 protein | Hs.30154 | N51514 | 8.894226 |
| LFNG | Lunatic fringe homolog | Hs.159142 | R56561 | 8.826694 |
| OMD | Osteomodulin | Hs.94070 | N32201 | 8.450854 |
| CHRFAM7A | CHRNA7 and FAM7A fusion | Hs.353211 | W93369 | 8.396351 |
| PDGFβ | Platelet-derived growth factor β polypeptide | Hs.1976 | W72000 | 8.303292 |
| ESTs | Hs.348762 | AA700772 | 8.011256 | |
| ESTs | Hs.323780 | N22836 | 7.949673 | |
| KIAA1211 | KIAA1211 protein | Hs.205293 | N35889 | 7.908669 |
| Homo sapiens cDNA FLJ12815 fis, clone NT2RP2002546 | Hs.49476 | AA284237 | 7.765829 | |
| ARVCF | Armadillo repeat gene deletes in velocardiofacial syndrome | Hs.171900 | H17198 | 7.637739 |
| CDH11 | Cadherin 11, type 2, OB-cadherin (osteoblast) | Hs.75929 | AA136983 | 7.589666 |
| CEP4 | Cdc42 effector protein 4; binder of Rho GTPases 4 | Hs.3903 | AA449061 | 7.490882 |
| MEOX1 | Mesenchyme homeo box 1 | Hs.438 | AA426311 | 7.461304 |
| APOD | Apolipoprotein D | Hs.75736 | H15842 | 7.457497 |
| PLG | Plasminogen | Hs.75576 | T73090 | 7.127251 |
| FZD7 | Frizzled homolog 7 | Hs.173859 | N69049 | 7.07609 |
| Homo sapiens, clone IMAGE:3450973, mRNA | Hs.7921 | AA620437 | 7.042933 | |
| SPRY2 | Sprouty homolog 2 | Hs.18676 | AA453759 | 7.038161 |
| ESTs | Hs.355694 | AA778653 | 6.995952 | |
| ESTs | Hs.164680 | AA463229 | 6.980936 | |
| POPX1 | Partner of PIX 1 | Hs.166351 | W40125 | 6.959919 |
| MS12 | Musashi homolog 2 | Hs.173179 | N45139 | 6.9322 |
| ABCA9 | ATP-binding cassette, sub-family A (ABC1), member 9 | Hs.301496 | AI822061 | 6.920054 |
| ESTs | Hs.268874 | R98003 | 6.890625 | |
| ELLS1 | Hypothetical protein Ells1 | Hs.7913 | N29882 | 6.860183 |
| KIAA0638 | KIAA0638 protein | Hs.77864 | AA405486 | 6.84359 |
| ABCA6 | ATP-binding cassette, sub-family A (ABC1), member 6 | Hs.15780 | AA099357 | 6.838837 |
| SEPT6 | Septin 6 | Hs.90998 | AA868745 | 6.75616 |
| ESTs | Hs.50162 | N67355 | 6.715135 | |
| SPAG9 | Sperm-associated antigen 9 | Hs.129872 | AA399253 | 6.580305 |
| KIAA0937 | KIAA0937 protein | Hs.62264 | AA487527 | 6.579918 |
| Homo sapiens clone 24628 mRNA sequence | Hs.129997 | AA885845 | 6.569535 | |
| KLF5 | Kruppel-like factor 5 (intestinal) | Hs.84728 | R27011 | 6.539115 |
| IL11RA | Interleukin 11 receptor, α | Hs.64310 | AI822086 | 6.526972 |
| FLJ90754 | Homo sapiens mRNA full-length insert cDNA clone | Hs.8963 | AA424560 | 6.520919 |
| ACVRL1 | Activin A receptor type II-like 1 | Hs.172670 | H42572 | 6.520158 |
| PTGFRN | Prostaglandin F2 receptor negative regulator | Hs.300591 | T83630 | 6.477428 |
| ESTs | Hs.247150 | AA459734 | 6.474894 | |
| DHRS6 | Oxidoreductase UCPA | Hs.124696 | R97516 | 6.466339 |
| TTYH2 | Tweety homolog 2 | Hs.27935 | AA434395 | 6.45494 |
| SCDGF-B | Spinal cord-derived growth factor-B | Hs.112885 | AA904948 | 6.433207 |
| DACT1 | Heptacellular carcinoma novel gene-3 protein | Hs.48950 | AA487274 | 6.426798 |
| GPM6B | Glycoprotein M6B | Hs.5422 | N59368 | 6.411646 |
| LZTS1 | Leucine zipper, putative tumor suppressor 1 | Hs.93605 | H09757 | 6.3579 |
| NRXN3 | Neurexin 3 | Hs.247837 | AA450335 | 6.285427 |
Input parameters for SAM analysis: imputation engine is “10-nearest neighbor imputer”; data type is “two class, unpaired data”; data are in log scale; number of permutations is 1000; No blocked permutations; RNG seed is 1234567; (delta, fold change) is (2.46002); (upper cutoff, lower cutoff) is (4.02194, −6.08331). Computed quantities are: computed exchangeability factor S0 is 236.1422; S0 percentile is 0; false significant number (median, 90%) is (0.57990, 0.57990); false discovery rate (median, 90%) is (0.19928, 0.19928); Pi0Hat is 0.5799.