Screening of lymph nodes metastasis associated lncRNAs in colorectal cancer patients

Table 1 Summary of data from long noncoding RNA microarray for three pairs of metastatic lymph nodes, normal lymph nodes and tumor tissue of colorectal cancer

Sample ID			lncRNA
			Fold change ≤ 4	Fold change > 4	Total	Changes lncRNA
R1	MLN vs NLN	Up-regulation	704	161	865	2087
		Down-regulation	1034	188	1222
	MLN vs tumor	Up-regulation	2864	1720	4584	9052
		Down-regulation	2421	2047	4468
	NLN vs tumor	Up-regulation	2915	1999	4914	8895
		Down-regulation	2303	1678	3981
R2	MLN vs NLN	Up-regulation	1223	354	1577	3923
		Down-regulation	1934	412	2346
	MLN vs tumor	Up-regulation	488	105	593	1109
		Down-regulation	457	59	516
	NLN vs tumor	Up-regulation	2123	763	2886	4514
		Down-regulation	1231	397	1628
R3	MLN vs NLN	Up-regulation	1557	399	1956	3707
		Down-regulation	1441	310	1751
	MLM vs tumor	Up-regulation	915	114	1029	1572
		Down-regulation	482	61	543
	NLN vs tumor	Up-regulation	1481	597	2078	3619
		Down-regulation	1102	439	1541

MLN: Metastatic lymph nodes; NLN: Normal lymph nodes; Tumor: Tumor tissue of colorectal cancer. lncRNA: Long noncoding RNA.

Table 2 Summary of data from message RNA microarray for three pairs of metastatic lymph nodes, normal lymph nodes and tumor tissue of colorectal cancer

Sample			Message RNA
ID			Fold change ≤ 4	Fold change > 4	Total	Changes lncRNA
R1	Positive vs negative	Up-regulation	1421	310	1731	2818
		Down-regulation	910	177	1087
	Positive vs tumor	Up-regulation	4028	2762	6790	10525
		Down-regulation	2112	1623	3735
	Negative vs tumor	Up-regulation	3848	2542	6390	9875
		Down-regulation	2088	1397	3485
R2	Positive vs negative	Up-regulation	1354	544	1898	4354
		Down-regulation	1960	496	2456
	Positive vs tumor	Up-regulation	571	129	700	1534
		Down-regulation	711	123	834
	Negative vs tumor	Up-regulation	1806	858	2664	5103
		Down-regulation	1692	747	2439
R3	Positive vs negative	Up-regulation	1706	612	2318	4317
		Down-regulation	1562	437	1999
	Positive vs tumor	Up-regulation	865	142	1007	1855
		Down-regulation	731	117	848
	Negative vs tumor	Up-regulation	1328	756	2084	4569
		Down-regulation	1681	804	2485

MLN: Metastatic lymph nodes; NLN: Normal lymph nodes; Tumor: Tumor tissue of colorectal cancer.

Table 3 Specifically expressed long noncoding RNAs in metastatic lymph nodes by comparing metastatic lymph nodes both with normal lymph nodes and tumor tissue of colorectal cancer

Up-regulated in MLN		Down-regulated in MLN
LncRNA	Log2 fold change (M > N and M > T)	LncRNA	Log2 fold change (M < N and M < T)
uc004aej.2	2.466393114	BC042589	-4.323467267
ENST00000393311	2.086153236	ENST00000429729	-2.720521004
ENST00000447552	2.795028512	uc002ztx.3	-2.196481477
AK025180	2.885255406	ENST00000418346	-2.260120093
AW449673	3.034259412	ENST00000465846	-3.200848076
ENST00000450572	2.06748042
ENST00000483126	2.357461429
ENST00000425785	2.055384542
CR599788	2.670107882
AK097728	2.453511443
uc002jsc.1	2.854856902
BC036914	6.696784453
AK021444	7.763431269
AK307796	3.345445171

Metastatic lymph nodes (MLN) samples vs normal lymph node samples and MLN samples vs colorectal cancer tumor tissue, false discovery rate, 0.1%, P = 0.01. M: Metastatic lymph nodes; N: Normal lymph node; T: Tumor tissue of colorectal cancer; LncRNA: Long noncoding RNA.

Table 4 Verification of expression levels of differentially expressed long noncoding RNAs in metastatic lymph nodes by quantitative real-time polymerase chain reaction in 26 colorectal cancer patients with lymph node metastasis

	AK307796/GAPDH			AK025180/GAPDH			AK021444/GAPDH			ENST00000465846/GAPDH
	MLN	NLN	Tumor	MLN	NLN	Tumor	MLN	NLN	Tumor	MLN	NLN	Tumor
R1	0.08760	0.03420	0.0358	0.0790	0.03480	0.03190	0.01370	0.00453	0.00735	0.02700	0.0347	0.06610
R2	0.06670	0.04090	0.0432	0.1340	0.07770	0.03870	0.00978	0.00225	0.00560	0.02120	0.0421	0.06440
R3	0.10417	0.04530	0.0524	0.0940	0.05300	0.04500	0.00762	0.00365	0.00435	0.02087	0.0334	0.05210
R4	0.04708	0.03990	0.0526	0.0800	0.06020	0.04938	0.01060	0.00415	0.00541	0.02900	0.0297	0.05370
R5	0.07200	0.03230	0.0608	0.0906	0.06860	0.05450	0.01030	0.00324	0.00608	0.02910	0.0390	0.06820
R6	0.07950	0.03850	0.0635	0.1310	0.06070	0.05690	0.01160	0.00363	0.00764	0.02015	0.0294	0.05900
R7	0.09710	0.03310	0.0401	0.0870	0.04520	0.03580	0.00813	0.00268	0.00455	0.02180	0.0303	0.05310
R8	0.05620	0.04024	0.0614	0.1110	0.07154	0.05544	0.00798	0.00427	0.00706	0.02680	0.0379	0.06635
R9	0.07110	0.03430	0.0414	0.0892	0.04750	0.03740	0.01320	0.00289	0.00495	0.02230	0.0315	0.06427
R10	0.06120	0.03910	0.0591	0.0923	0.04680	0.05233	0.00834	0.00308	0.00751	0.02520	0.0369	0.05480
R11	0.08980	0.04270	0.0398	0.1200	0.07313	0.03980	0.01340	0.00448	0.00508	0.02390	0.0325	0.06177
R12	0.06250	0.04133	0.0605	0.0827	0.07010	0.03670	0.00780	0.00397	0.00562	0.02638	0.0355	0.05610
R13	0.10250	0.03570	0.0423	0.1050	0.04990	0.05060	0.01270	0.00319	0.00683	0.02310	0.0339	0.05690
R14	0.05850	0.03592	0.0537	0.1070	0.05150	0.05470	0.01310	0.00408	0.00697	0.02556	0.0389	0.06105
R15	0.04981	0.03490	0.0449	0.0983	0.06360	0.04074	0.00883	0.00313	0.00719	0.02497	0.0331	0.05940
R16	0.09623	0.03680	0.0630	0.0962	0.05080	0.04980	0.00847	0.00375	0.00463	0.02350	0.0383	0.06370
R17	0.08120	0.04080	0.0507	0.1030	0.06750	0.04230	0.01210	0.00335	0.00652	0.02090	0.0305	0.06010
R18	0.07800	0.03623	0.0627	0.0839	0.04820	0.04850	0.01240	0.00367	0.00478	0.02860	0.0365	0.06505
R19	0.09910	0.03800	0.0462	0.1140	0.07084	0.04472	0.00932	0.00349	0.00531	0.02050	0.0311	0.05750
R20	0.08452	0.03524	0.0566	0.0998	0.05473	0.04634	0.01160	0.00381	0.00736	0.02475	0.0363	0.06810
R21	0.09110	0.04210	0.0437	0.0815	0.06680	0.04360	0.00956	0.00341	0.00759	0.02410	0.0318	0.05530
R22	0.06780	0.03794	0.0521	0.1160	0.06154	0.04740	0.00868	0.00403	0.00592	0.02600	0.0391	0.06287
R23	0.09380	0.04392	0.0475	0.1210	0.05823	0.04580	0.01250	0.00275	0.00578	0.02430	0.0329	0.05450
R24	0.06781	0.03900	0.0553	0.0881	0.06014	0.05143	0.00907	0.00441	0.00622	0.02730	0.0376	0.06590
R25	0.07430	0.04180	0.0491	0.1150	0.05680	0.04150	0.01190	0.00295	0.00517	0.02279	0.0309	0.05830
R26	0.05320	0.03753	0.0579	0.1020	0.06840	0.05630	0.01290	0.00421	0.00636	0.02813	0.0385	0.06668

MLN: Metastatic lymph nodes; NLN: Normal lymph nodes; Tumor: Tumor tissue of colorectal cancer; GAPDH: Glyceraldehyde-3-phosphate dehydrogenase.