Table 3.
Genes with higher expression in MSLCL samples. All genes with an increased expression according to RNAseq analysis in at least 25% of MS samples, never exceeded by any control (co) were listed. The AUC ± SE were determined and the FPKM at 100% specificity was taken as the cut-off value for predicting MS. Statistics: p values from unpaired t-test were adjusted by multiple correction using Bonferroni–Dunn method. The false discovery rate (FDR) was calculated by Benjamini–Hochberg method. Genes were ranked according to their adjusted p value.
| Name | Mean (co) n = 20 [FPKM] |
Mean (MS) n = 59 [FPKM] | p Value | Adjusted p Value (Bonferroni–Dunn) | FDR q Value (Benjamini–Hochberg) | AUC ± SE | Cut-Off [FPKM] at 100% Specificity |
|---|---|---|---|---|---|---|---|
| MT-TY | 24.09 | 55.71 | 0.00003 | 0.0011 | 0.0006 | 0.790 ± 0.056 | 67.83 |
| MT-TC | 146.6 | 417.2 | 0.00004 | 0.0013 | 0.0006 | 0.847 ± 0.046 | 355.7 |
| AL669831.1 | 0.1678 | 0.2549 | 0.00005 | 0.0017 | 0.0006 | 0.800 ± 0.052 | 0.277 |
| MT-TE | 4.012 | 9.250 | 0.00007 | 0.0024 | 0.0006 | 0.790 ± 0.053 | 10.39 |
| LINC01529 | 0.0394 | 0.1054 | 0.00010 | 0.0034 | 0.0006 | 0.797 ± 0.052 | 0.119 |
| AL365273.1 | 1.442 | 2.960 | 0.00010 | 0.0034 | 0.0006 | 0.773 ± 0.058 | 3.426 |
| SNORA79B | 0.2844 | 0.7127 | 0.00019 | 0.0065 | 0.0009 | 0.800 ± 0.053 | 0.807 |
| MIR34AHG | 0.4675 | 0.9528 | 0.00033 | 0.0116 | 0.0014 | 0.743 ± 0.062 | 1.189 |
| ENTPD1-AS1 | 0.3070 | 0.5408 | 0.00037 | 0.0129 | 0.0014 | 0.761 ± 0.059 | 0.622 |
| MFSD14C | 0.7940 | 1.0780 | 0.00039 | 0.0137 | 0.0014 | 0.748 ± 0.060 | 1.263 |
| RNU7-20P | 0.2588 | 0.7819 | 0.00071 | 0.0247 | 0.0022 | 0.780 ± 0.055 | 1.016 |
| REELD1 | 0.0213 | 0.0683 | 0.00076 | 0.0265 | 0.0022 | 0.791 ± 0.053 | 0.081 |
| MT-TG | 6.905 | 14.600 | 0.00088 | 0.0307 | 0.0022 | 0.734 ± 0.062 | 19.16 |
| GABARAP | 0.2457 | 0.5464 | 0.00088 | 0.0308 | 0.0022 | 0.757 ± 0.059 | 0.616 |
| SNORD20 | 0.6918 | 1.5220 | 0.00107 | 0.0375 | 0.0025 | 0.747 ± 0.060 | 2.164 |
| AL669831.3 | 0.0185 | 0.0411 | 0.00178 | 0.0622 | 0.0039 | 0.729 ± 0.063 | 0.049 |
| RF00012 | 0.0564 | 0.1735 | 0.00219 | 0.0766 | 0.0045 | 0.775 ± 0.055 | 0.217 |
| MPL | 0.0084 | 0.0188 | 0.00234 | 0.0817 | 0.0045 | 0.726 ± 0.060 | 0.024 |
| FAM89B | 0.5908 | 0.8061 | 0.00743 | 0.2599 | 0.0137 | 0.701 ± 0.060 | 0.946 |
| AC006001.3 | 0.5246 | 0.6044 | 0.00847 | 0.2963 | 0.0141 | 0.721 ± 0.058 | 0.657 |
| EBF2 | 0.0007 | 0.0024 | 0.00849 | 0.2970 | 0.0141 | 0.696 ± 0.059 | 0.004 |
| CFAP73 | 0.0359 | 0.0552 | 0.00998 | 0.3491 | 0.0159 | 0.699 ± 0.062 | 0.063 |
| LINC01118 | 0.0050 | 0.0120 | 0.01080 | 0.3781 | 0.0164 | 0.682 ± 0.060 | 0.016 |
| HERV-K 3p12.3 | 0.1862 | 0.2447 | 0.01254 | 0.4390 | 0.0177 | 0.637 ± 0.061 | 0.334 |
| DLG1-AS1 | 0.0023 | 0.0103 | 0.01262 | 0.4416 | 0.0177 | 0.664 ± 0.063 | 0.016 |
| DIAPH2-AS1 | 0.0130 | 0.0321 | 0.01402 | 0.4908 | 0.0189 | 0.713 ± 0.059 | 0.033 |
| RPL41P1 | 133.8 | 317.3 | 0.01642 | 0.5746 | 0.0212 | 0.675 ± 0.062 | 276.9 |
| MIR3150BHG | 0.0372 | 0.1018 | 0.01693 | 0.5924 | 0.0212 | 0.680 ± 0.059 | 0.102 |
| TTLL7-IT1 | 0.0022 | 0.0109 | 0.02014 | 0.7048 | 0.0243 | 0.704 ± 0.059 | 0.009 |
| RNU6-32P | 0.0636 | 0.1835 | 0.02500 | 0.8751 | 0.0292 | 0.670 ± 0.062 | 0.273 |
| GOLGA6L4 | 0.0004 | 0.0041 | 0.02800 | 0.9798 | 0.0316 | 0.736 ± 0.055 | 0.002 |
| HIST2H2AC | 0.8899 | 1.21 | 0.06537 | >0.999999 | 0.0654 | 0.606 ± 0.065 | 1.379 |
| C3P1 | 0.0014 | 0.0045 | 0.02933 | >0.999999 | 0.0321 | 0.659 ± 0.062 | 0.005 |
| MIR221 | 0.4966 | 0.9103 | 0.03409 | >0.999999 | 0.0351 | 0.614 ± 0.064 | 1.158 |
| HERV-K11 | 0.2805 | 0.3140 | 0.03055 | >0.999999 | 0.0324 | 0.683 ± 0.064 | 0.303 |