Comprehensive analysis of a long noncoding RNA-associated competing endogenous RNA network in colorectal cancer

Figures & data

Table 1 Clinicopathological characteristics of 539 CRC patients

Clinicopathological characteristics	Patients (N=539)
	n	%
Age category (years)
<65	220	40.82
≥65	319	59.18
Gender
Female	252	46.75
Male	287	53.25
Pathological stage
Stage I	99	18.37
Stage II	192	35.62
Stage III	163	30.24
Stage IV	85	15.77
Pathologic T
Tis	1	0.18
T1	18	3.34
T2	95	17.63
T3	360	66.79
T4	65	12.06
Pathologic N
N0	301	55.85
N1	138	25.60
N2	100	18.55
Pathologic M
M0	404	74.95
M1	83	15.40
Mx	52	9.65
Survival status
Alive	440	81.63
Dead	99	18.37

Abbreviation: CRC, colorectal cancer.

Figure 1 Flowchart of the lncRNA–miRNA–mRNA ceRNA network analysis.

Figure 2 Heatmaps based on the differentially expressed RNAs in CRC and normal tissues.

Notes: (A) The heatmap with top 100 upregulated and top 100 downregulated mRNAs. (B) The heatmap with top 100 upregulated and top 100 downregulated lncRNAs. (C) The heatmap with all the DEmiRNAs.
Abbreviation: CRC, colorectal cancer.

Table 2 The top 11 DElncRNAs putatively targeted by most DEmiRNAs in the ceRNA network

DElncRNAs	DEmiRNAs
KCNQ1OT1	hsa-mir-106a, hsa-mir-141, hsa-mir-143, hsa-mir-145, hsa-mir-150, hsa-mir-152, hsa-mir-17, hsa-mir-182, hsa-mir-192, hsa-mir-193b, hsa-mir-206, hsa-mir-217, hsa-mir-223, hsa-mir-301b, hsa-mir-32, hsa-mir-338, hsa-mir-372, hsa-mir-375, hsa-mir-424, hsa-mir-429, hsa-mir-454, hsa-mir-96, hsa-mir-98
ADAMTS9-AS2	hsa-mir-106a, hsa-mir-141, hsa-mir-143, hsa-mir-144, hsa-mir-145, hsa-mir-150, hsa-mir-152, hsa-mir-182, hsa-mir-193b, hsa-mir-223, hsa-mir-301b, hsa-mir-32, hsa-mir-338, hsa-mir-372, hsa-mir-375, hsa-mir-454, hsa-mir-96, hsa-mir-98
DLX6-AS1	hsa-mir-106a, hsa-mir-141, hsa-mir-144, hsa-mir-145, hsa-mir-150, hsa-mir-152, hsa-mir-17, hsa-mir-192, hsa-mir-193b, hsa-mir-206, hsa-mir-223, hsa-mir-338, hsa-mir-372, hsa-mir-424, hsa-mir-429
AGAP11	hsa-mir-106a, hsa-mir-141, hsa-mir-143, hsa-mir-145, hsa-mir-150, hsa-mir-152, hsa-mir-17, hsa-mir-182, hsa-mir-193b, hsa-mir-206, hsa-mir-21, hsa-mir-217, hsa-mir-372, hsa-mir-375, hsa-mir-424
AC010336.2	hsa-mir-106a, hsa-mir-141, hsa-mir-144, hsa-mir-145, hsa-mir-150, hsa-mir-17, hsa-mir-182, hsa-mir-192, hsa-mir-193b, hsa-mir-338, hsa-mir-372, hsa-mir-429
LINC00461	hsa-mir-106a, hsa-mir-141, hsa-mir-143, hsa-mir-144, hsa-mir-145, hsa-mir-150, hsa-mir-192, hsa-mir-32, hsa-mir-338, hsa-mir-372, hsa-mir-424, hsa-mir-96
LINC00484	hsa-mir-106a, hsa-mir-141, hsa-mir-143, hsa-mir-152, hsa-mir-206, hsa-mir-217, hsa-mir-223, hsa-mir-32, hsa-mir-338, hsa-mir-372, hsa-mir-424, hsa-mir-98
LIFR-AS1	hsa-mir-106a, hsa-mir-144, hsa-mir-150, hsa-mir-182, hsa-mir-192, hsa-mir-193b, hsa-mir-206, hsa-mir-32, hsa-mir-372, hsa-mir-375, hsa-mir-96
LINC00330	hsa-mir-106a, hsa-mir-145, hsa-mir-150, hsa-mir-17, hsa-mir-192, hsa-mir-206, hsa-mir-301b, hsa-mir-372, hsa-mir-424, hsa-mir-454, hsa-mir-98
FAM95B1	hsa-mir-141, hsa-mir-143, hsa-mir-150, hsa-mir-152, hsa-mir-182, hsa-mir-206, hsa-mir-338, hsa-mir-375, hsa-mir-96, hsa-mir-98
PVT1	hsa-mir-106a, hsa-mir-143, hsa-mir-145, hsa-mir-150, hsa-mir-152, hsa-mir-17, hsa-mir-21, hsa-mir-217, hsa-mir-372, hsa-mir-424

Table 3 The 25 DEmiRNAs with their target DEmRNAs in the ceRNA network

DEmiRNAs	DEmRNAs
hsa-mir-106a	CFL2, FOXQ1, FAM129A, CADM2, FJX1
hsa-mir-141	ELAVL4, PHLPP2, EPHA7, KIAA1549
hsa-mir-143	COL1A1, SERPINE1
hsa-mir-144	KCNQ5, GRIK3
hsa-mir-145	SERPINE1
hsa-mir-150	EREG, HILPDA, SLC7A11
hsa-mir-152	BMP3, NPTX1, KLF4
hsa-mir-17	FAM46C, FOXQ1, FJX1, CADM2, CYBRD1, FAM129A, CFL2
hsa-mir-182	CHL1, NPTX1, ULBP2
hsa-mir-192	GRHL1
hsa-mir-193b	PLAU
hsa-mir-206	STC2, SFRP1
hsa-mir-21	TGFBI
hsa-mir-217	DACH1
hsa-mir-223	EPB41L3
hsa-mir-301b	RBM20, CFL2
hsa-mir-32	PHLPP2, PBLD, PAX9, UGP2
hsa-mir-338	NOVA1
hsa-mir-372	CADM2, TMEM100, SLC7A11, MIXL1
hsa-mir-375	ELAVL4
hsa-mir-424	PSAT1, TMEM100, PHLPP2, CBX2, AXIN2, TPM2
hsa-mir-429	PMAIP1
hsa-mir-454	CFL2, RBM20
hsa-mir-96	ALK, TRIB3, SLC1A1
hsa-mir-98	HAND1, IGF2BP1, PRSS22, RGS16, TRIM71, IGF2BP3, CPA4

Figure 3 The lncRNA–miRNA–mRNA ceRNA network in CRC.

Notes: Red rounds represent upregulated DEmRNAs and blue rounds represent downregulated DEmRNAs. Red squares represent upregulated DElncRNAs and blue squares represent downregulated DElncRNAs. Green triangles represent upregulated DEmiRNAs and yellow triangles represent downregulated DEmiRNAs.
Abbreviation: CRC, colorectal cancer.

Figure 4 Linear regression of ceRNA expression levels for LINC00461.

Notes: LINC00461 vs (A) CADM2, (B) GRIK3, (C) ELAVL4, (D) FAM129A, (E) CFL2, (F) TMEM100, (G) NOVA1, (H) TPM2, and (I) MIXL1. The red line represents the linear model fitted by the dots in each figure, while green lines represent the 95% CI. “Cor” represents the correlation between the expressions of LINC00461 and the specific mRNA.

Figure 5 Linear regression of ceRNA expression levels for LINC00484.

Notes: LINC00484 vs (A) BMP3, (B) UGP2, (C) PHLPP2, (D) KLF4, (E) PBLD, (F) EPB41L3, (G) TMEM100, and (H) SFRP1. The red line represents the linear model fitted by the dots in each figure while green lines represent the 95% CI. “Cor” represents the correlation between the expressions of LINC00484 and the specific mRNA.

Figure 6 Kaplan–Meier survival curves for the two DElncRNAs significantly associated with overall survival of CRC patients. Note: Kaplan–Meier survival curves for (A) AP004609.1 and (B) C2orf48.

Abbreviation: CRC, colorectal cancer.

Figure 7 Kaplan–Meier survival curves for the five DEmiRNAs significantly associated with overall survival of CRC patients.

Note: Kaplan–Meier survival curves for (A) hsa-mir-96, (B) hsa-mir-144, (C) hsa-mir-145, (D) hsa-mir-193b, and (E) hsa-mir-375.
Abbreviation: CRC, colorectal cancer.

Figure 8 Kaplan–Meier survival curves for the six DEmRNAs significantly associated with overall survival of CRC patients.

Note: Kaplan–Meier survival curves for (A) FAM46C, (B) FJX1, (C) HAND1, (D) SERPINE1, (E) TPM2, and (F) ULBP2.
Abbreviation: CRC, colorectal cancer.

Table 4 The correlations between DElncRNAs from the ceRNA network and clinical features of CRC patients

Comparisons	Upregulated	Downregulated
Gender (male vs female)		AC110491.1
N stage (N1 + N2 vs N0)	H19	HULC
M stage (M1 vs M0)	CLDN10-AS1, H19	HULC
Pathological stage (III + IV vs I + II)	H19	HULC

Abbreviation: CRC, colorectal cancer.

Table 5 The top 10 predominant BP terms and all the four CC terms and MF terms in GO functional enrichment analysis

Categories	Terms	Count	P-value
GO BP	GO:0045892~negative regulation of transcription, DNA-templated	7	3.16 E–03
	GO:0048147~negative regulation of fibroblast proliferation	3	3.68 E–03
	GO:0001525~angiogenesis	5	4.02 E–03
	GO:0043434~response to peptide hormone	3	7.30 E–03
	GO:0071363~cellular response to growth factor stimulus	3	7.62 E–03
	GO:0050680~negative regulation of epithelial cell proliferation	3	0.012
	GO:0017148~negative regulation of translation	3	0.012
	GO:0001957~intramembranous ossification	2	0.017
	GO:0042035~regulation of cytokine biosynthetic process	2	0.020
	GO:0060346~bone trabecula formation	2	0.023
GO CC	GO:0005615~extracellular space	13	1.79 E–04
	GO:0070062~extracellular exosome	14	0.031
	GO:0005886~plasma membrane	18	0.036
	GO:0031012~extracellular matrix	4	0.045
GO MF	GO:0003730~mRNA 3′-UTR binding	3	8.90 E–03
	GO:0045182~translation regulator activity	2	0.017
	GO:0048027~mRNA 5′-UTR binding	2	0.026
	GO:0001190~transcriptional activator activity, RNA polymerase II transcription factor binding	2	0.045

Abbreviations: BP, biological process; CC, cellular component; GO, Gene Ontology; MF, molecular function; UTR, untranslated region.

Table 6 KEGG pathways enriched by the DEmRNAs in the ceRNA network

ID	Terms	P-value
hsa04550	Signaling pathways regulating pluripotency of stem cells	3.51 E–03
hsa04115	p53 signaling pathway	9.51 E–03
hsa04610	Complement and coagulation cascades	0.012
hsa00750	Vitamin B6 metabolism	0.014
hsa04974	Protein digestion and absorption	0.016
hsa05206	MicroRNAs in cancer	0.019
hsa04933	AGE-RAGE signaling pathway in diabetic complications	0.020
hsa04724	Glutamatergic synapse	0.024
hsa04310	Wnt signaling pathway	0.036
hsa04390	Hippo signaling pathway	0.041

Abbreviation: KEGG, Kyoto Encyclopedia of Genes and Genomes.

Table S1 All the 64 DElncRNAs in the ceRNA network

DElncRNAs	Ensembl ID	Log2FC	FDR	DElncRNAs	Ensembl ID	Log2FC	FDR
ABCA9-AS1	ENSG00000231749	3.9864	1.50E–03	ERVMER61-1	ENSG00000230426	6.2730	4.00E–03
AC007384.1	ENSG00000237513	−2.4205	6.92E–14	FAM95B1	ENSG00000223839	−2.0743	4.64E–06
AC009065.1	ENSG00000259780	2.4120	7.23E–03	FRMD6-AS2	ENSG00000258537	−3.1025	7.09E–09
AC009093.1	ENSG00000259807	3.0580	8.28E–05	GAS6-AS1	ENSG00000233695	3.5499	1.09E–07
AC009336.1	ENSG00000272729	−2.0597	6.03E–06	H19	ENSG00000130600	4.1017	5.86E–04
AC010336.2	ENSG00000260500	−2.7897	2.57E–14	HCG23	ENSG00000228962	−2.5508	3.36E–13
AC012640.1	ENSG00000248968	2.4459	2.90E–04	HULC	ENSG00000251164	6.8799	6.67E–03
AC016745.1	ENSG00000234997	3.6141	4.61E–03	JAZF1-AS1	ENSG00000234336	−2.6263	2.05E–13
AC020907.1	ENSG00000179066	3.8949	3.35E–03	KCNQ1-AS1	ENSG00000229414	2.53016	6.52E–03
AC064836.2	ENSG00000272966	2.5934	4.09E–03	KCNQ1OT1	ENSG00000269821	2.0209	1.35E–05
AC084262.1	ENSG00000260253	3.2217	4.57E–03	LIFR-AS1	ENSG00000244968	−2.3659	2.13E–13
AC110491.1	ENSG00000261292	−4.8260	3.22E–22	LINC00092	ENSG00000225194	−2.8438	8.99E–30
ADAMTS9-AS1	ENSG00000241158	−3.9253	2.66E–28	LINC00330	ENSG00000235097	−2.9422	1.32E–07
ADAMTS9-AS2	ENSG00000241684	−2.8713	5.15E–21	LINC00402	ENSG00000235532	−2.7266	1.25E–09
AGAP11	ENSG00000271880	−2.1666	1.83E–07	LINC00460	ENSG00000233532	6.2479	1.30E–08
AL138995.1	ENSG00000277763	−2.4069	1.42E–17	LINC00461	ENSG00000245526	−2.9817	1.73E–13
AL161431.1	ENSG00000275216	5.7502	7.72E–07	LINC00473	ENSG00000223414	−3.3201	6.64E–17
AL360004.1	ENSG00000196979	−2.3594	1.39E–06	LINC00484	ENSG00000229694	−3.1173	2.08E–16
AL512652.1	ENSG00000275485	2.02862	2.74E–04	LINC00488	ENSG00000214381	−3.1742	1.39E–10
AL513123.1	ENSG00000236347	3.0582	5.80E–05	LINC00507	ENSG00000256193	−4.1785	5.34E–24
AL590483.1	ENSG00000229960	2.8803	7.85E–06	LMO7-AS1	ENSG00000261105	2.4135	6.21E–05
AP000553.1	ENSG00000272954	3.3636	2.14E–05	MIR22HG	ENSG00000186594	−2.0251	9.64E–22
AP002478.1	ENSG00000266401	4.3909	1.13E–04	MYO16-AS1	ENSG00000236242	3.8592	6.26E–03
AP004609.1	ENSG00000245869	−2.0890	7.59E–05	PCAT1	ENSG00000253438	2.4776	4.83E–07
C17orf77	ENSG00000182352	4.1557	1.43E–03	POU6F2-AS1	ENSG00000224122	5.8205	4.29E–03
C20orf166-AS1	ENSG00000174403	−3.4682	8.37E–20	PVT1	ENSG00000249859	2.6328	2.82E–18
C2orf48	ENSG00000163009	2.2264	3.27E–05	PWRN1	ENSG00000259905	−2.2617	1.55E–04
C7orf69	ENSG00000136275	3.2131	9.71E–03	RBMS3-AS3	ENSG00000235904	−2.7161	1.60E–13
CLDN10-AS1	ENSG00000223392	4.5630	6.72E–04	SFTA1P	ENSG00000225383	−2.7508	1.59E–11
CRNDE	ENSG00000245694	4.4129	1.47E–12	ST7-OT4	ENSG00000214188	2.4463	6.43E–04
DLX6-AS1	ENSG00000231764	4.3820	1.38E–03	UCA1	ENSG00000214049	3.9110	1.06E–04
EGOT	ENSG00000235947	2.3163	2.49E–03	WASIR2	ENSG00000231439	2.1913	8.49E–03

Abbreviations: FDR, false discovery rate; log₂FC, log₂fold change.