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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

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