Skip to main content

Advertisement

Table 1 Top 20 significant genes from paired and unpaired lncDIFF analysis for TCGA HNSC study. The overlap of genes are in bold. Likelihood Ratio Test statistics, p-value and FDR are output from lncDIFF

From: lncDIFF: a novel quasi-likelihood method for differential expression analysis of non-coding RNA

Gene Paired Tumor vs Normal Statistics FDR Gene Unpaired Tumor vs Normal Statistics FDR
Ensembl ID Log2 Fold Change Ensembl ID Log2 Fold Change
ERVH48–1 ENSG00000233056.1 0.415 211.767 7.48E-45 HCG22 ENSG00000228789.2 −2.979 674.029 1.76E-145
LINC02487 ENSG00000203688.4 −3.747 200.441 1.11E-42 LINC02487 ENSG00000203688.4 −3.470 625.994 2.46E-135
HCG22 ENSG00000228789.2 −3.138 151.425 3.73E-32 MYHAS ENSG00000272975.1 −0.935 324.216 7.70E-70
LINC00668 ENSG00000265933.1 2.189 148.534 1.20E-31 LINC01405 ENSG00000185847.3 −1.366 276.487 1.45E-59
LINC02582 ENSG00000261780.2 1.027 144.294 8.10E-31 FALEC ENSG00000228126.1 − 1.721 252.647 1.82E-54
LINC00941 ENSG00000235884.2 2.450 138.020 1.59E-29 TMEM238L ENSG00000263429.3 −2.250 235.559 8.06E-51
LINC00942 ENSG00000249628.2 1.105 128.195 1.92E-27 AC005392.2 ENSG00000231412.2 −2.342 198.936 6.73E-43
LINC01234 ENSG00000249550.2 1.755 121.173 5.79E-26 AC140479.4 ENSG00000261760.2 −1.471 188.314 1.23E-40
LINC02154 ENSG00000235385.1 2.099 120.529 7.12E-26 ERVH48–1 ENSG00000233056.1 0.444 185.507 4.47E-40
AC134312.5 ENSG00000261327.3 2.064 115.828 6.85E-25 AC091563.1 ENSG00000254343.2 −2.185 174.352 1.10E-37
AL365181.2 ENSG00000272068.1 1.191 111.605 5.24E-24 LINC02582 ENSG00000261780.2 1.009 161.008 8.19E-35
DUXAP9 ENSG00000225210.5 2.868 110.895 6.87E-24 LINC00668 ENSG00000265933.1 1.626 154.270 2.23E-33
DUXAP8 ENSG00000206195.6 2.422 105.798 8.30E-23 ACBD3-AS1 ENSG00000234478.1 −1.733 150.782 1.08E-32
SFTA1P ENSG00000225383.2 1.676 103.239 2.80E-22 LINC00941 ENSG00000235884.2 2.090 150.692 1.08E-32
AC010343.3 ENSG00000250697.1 1.838 101.397 6.63E-22 AC134312.5 ENSG00000261327.3 2.146 150.725 1.08E-32
ELFN1-AS1 ENSG00000236081.1 1.590 101.238 6.74E-22 DUXAP9 ENSG00000225210.5 2.711 141.890 8.49E-31
LINC00520 ENSG00000258791.3 1.570 98.359 2.71E-21 ABHD11 ENSG00000225969.1 −1.730 140.148 1.92E-30
AC134312.2 ENSG00000260162.2 1.912 98.157 2.84E-21 AL365181.2 ENSG00000272068.1 1.008 138.932 3.35E-30
AC114956.2 ENSG00000248554.1 3.038 96.948 4.95E-21 DUXAP8 ENSG00000206195.6 2.230 134.501 2.95E-29
CASC9 ENSG00000249395.2 4.019 91.046 9.28E-20 AC134312.2 ENSG00000260162.2 1.982 129.028 4.42E-28