Table 3. Top 25 differentially expressed lncRNAs in TSCC samples.

Top 25 up-regulated lncRNAs						Top 25 down-regulated lncRNAs
lncRNA	Description	logFC	logCPM	PValue	FDR	lncRNA	Description	logFC	logCPM	PValue	FDR
LINC02081	S-phase cancer associated transcript 1	6.55907	8.288038	1.91E–17	6.25E–15	LINC01482	Long intergenic non-protein coding RNA 1482	−4.74187	5.152461	1.46E–46	1.05E–42
HOXC-AS2	HOXC cluster antisense RNA 2	4.769257	6.822429	1.98E–16	6.23E–14	LINC01829	long intergenic non-protein coding RNA 1829	−6.36522	6.723502	3.81E–39	1.38E–35
ZFPM2-AS1	ZFPM2 antisense RNA 1	6.665231	8.995423	6.58E–16	1.83E–13	AC027130.1	Antisense	−5.97661	4.460428	1.08E–36	2.61E–33
GSEC	G-quadruplex forming sequence containing lncRNA	3.169551	8.755699	2.53E–15	5.70E–13	LINC02160	long intergenic non-protein coding RNA 2160	−6.54927	4.019298	2.85E–35	5.15E–32
AL358334.2	novel transcript	5.390387	8.490721	3.08E–15	6.73E–13	RMST	rhabdomyosarcoma 2 associated transcript	−5.26688	3.845394	2.79E–32	4.03E–29
AC114956.2	novel transcript	4.310233	8.004771	2.70E–14	5.13E–12	AC010425.1	novel transcript	−5.48585	3.476603	1.74E–26	2.10E–23
FOXD2-AS1	adjacent opposite strand RNA 1	2.583099	8.660159	1.58E–13	2.60E–11	LINC01798	long intergenic non-protein coding RNA 1798	−3.58562	4.324626	8.21E–26	8.46E–23
AC114956.1	novel transcript	4.215066	6.515797	5.15E–13	7.91E–11	LINC01797	long intergenic non-protein coding RNA 1797	−6.20978	3.390637	1.23E–24	1.11E–21
HOXA10-AS	HOXA10 antisense RNA	5.742475	5.845017	1.66E–12	2.36E–10	FOXCUT	FOXC1 upstream transcript	−4.07718	5.643834	6.56E–24	5.26E–21
LINC02577	long intergenic non-protein coding RNA 2577	6.002243	9.022875	1.04E–11	1.20E–09	SALRNA1	senescence associated long non-coding RNA 1	−3.08355	5.220263	1.34E–20	9.64E–18
LINC00460	long intergenic non-protein coding RNA 460	6.495702	7.974214	2.49E–11	2.68E–09	AC005165.1	uncharacterized LOC646588	−4.48757	6.872983	4.67E–20	3.06E–17
AC134312.5	novel transcript	4.486535	7.851042	4.56E–11	4.28E–09	AL451062.1	Antisense	−4.06772	5.687606	1.08E–19	6.49E–17
LBX2-AS1	LBX2 antisense RNA 1	2.21821	9.536711	6.89E–11	6.14E–09	LINC00844	long intergenic non-protein coding RNA 844	−4.33944	3.690738	2.61E–19	1.45E–16
AC005041.3	novel transcript, antisense to LBX2	2.306235	5.550463	8.96E–11	7.79E–09	LINC01405	long intergenic non-protein coding RNA 1405	−4.17211	8.680984	2.83E–19	1.45E–16
LINC01633	long intergenic non-protein coding RNA 1633	5.183034	4.912757	1.17E–10	9.92E–09	AC116345.1	novel transcript	−3.55372	5.032557	3.01E–19	1.45E–16
AL513123.1	novel transcript	4.39058	5.896268	1.55E–10	1.26E–08	AL359715.1	novel transcript	−2.78923	5.706472	4.44E–19	2.00E–16
AL139147.1	novel transcript, antisense to SGIP1	7.261896	5.873938	1.82E–10	1.44E–08	AC009041.2	novel transcript	−2.81453	7.784602	2.09E–18	8.87E–16
U62317.1	uncharacterized LOC105373098	3.307612	10.06709	2.88E–10	2.19E–08	NKAIN3-IT1	NKAIN3 intronic transcript	−4.26922	5.38921	3.62E–18	1.40E–15
HOTAIR	HOX transcript antisense RNA	4.576517	6.201958	3.63E–10	2.73E–08	HSD52	uncharacterized LOC729467	−3.84183	3.899436	3.69E–18	1.40E–15
LINC01615	long intergenic non-protein coding RNA 1615	4.411259	9.631277	4.36E–10	3.21E–08	LINC02343	long intergenic non-protein coding RNA 2343	−5.54729	3.466708	6.86E–18	2.48E–15
SLC12A5-AS1	SLC12A5 and MMP9 antisense RNA 1	3.954435	6.183039	4.91E–10	3.54E–08	AL161668.4	novel transcript	−3.7574	4.738385	7.66E–18	2.63E–15
AC113346.1	novel transcript	5.684313	5.792491	5.03E–10	3.60E–08	SOX9-AS1	SOX9 antisense RNA 1	−2.54064	7.026463	2.56E–16	7.70E–14
LINC00941	long intergenic non-protein coding RNA 941	4.33015	8.913483	5.20E–10	3.68E–08	ZNF710-AS1	ZNF710 antisense RNA 1	−2.32401	9.970743	6.09E–16	1.76E–13
RNF144A-AS1	RNF144A antisense RNA 1	3.391581	7.876758	7.03E–10	4.83E–08	DRAIC	downregulated RNA in cancer, inhibitor of cell invasion and migration	−2.84397	5.017242	7.74E–16	2.07E–13
LINC01614	long intergenic non-protein coding RNA 1614	7.771486	8.166619	1.24E–09	8.26E–08	AC002401.3	novel transcript, antisense to PDK2	−3.1933	3.763892	1.10E–15	2.84E–13