Identification and prediction of novel non-coding and coding RNA-associated competing endogenous RNA networks in colorectal cancer

Table 1 Putative differentially expressed long-noncoding RNAs that may target differentially expressed microRNAs

DEmiRNAs	DElncRNAs	DEmiRNAs	DElncRNAs
Hsa-miR-193b	IGF2-AS, H19, MIR31HG, WT1-AS, MUC19, UCA1, POU6F2-AS1, TSSC1-IT1, MRPL23-AS1, SPATA13-AS1, HOTAIR, WASIR2, DLX6-AS1, CRNDE, MALAT1, KCNQ1OT1	Hsa-miR-182	AC009336.1, C5orf64, AL360004.1, AC010336.2, SFTA1P, LINC00402, RBMS3-AS3, ADAMTS9-AS2, LIFR-AS1, FRMD6-AS2
Hsa-miR-145	SHANK2-AS3, WT1-AS, MUC19, ST7-AS2, MRPL23-AS1, FAM155A-IT1, FAM41C, MIR205HG, DLX6-AS1, OSBPL10-AS1, ERVH48-1, CRNDE, PVT1, LINC00491, MALAT1, NKX2-1-AS1, KCNQ1OT1, AL139147.1, ITCH-IT1, LINC00452	Hsa-miR-106a	C20orf166-AS1, AC010336.2, HCG23, JAZF1-AS1, LINC00484, ADAMTS9-AS2, ARHGEF26-AS1, LIFR-AS1, LINC00461, LINC00507
Hsa-miR-187	SHANK2-AS3, MUC19, BTBD9-AS1, LINC00452, FAM41C, ATP11A-AS1, ERVH48-1, POU6F2-AS2, ARHGEF26-AS1, PVT1	Hsa-miR-152	C5orf64, AL360004.1, FAM95B1, LINC00484, ADAMTS9-AS2
Hsa-miR-150	IGF2-AS, C2orf48, SHANK2-AS3, C15orf54, HECW1-IT1, LINC00523, MUC19, ST7-OT4, CLDN10-AS1, TSSC1-IT1, MRPL23-AS1, BTBD9-AS1, LINC00355, LMO7-AS1, HOTAIR, MIR205HG, WASIR2, DLX6-AS1, LINC00460, LATS2-AS1, BOK-AS1, DSCAM-AS1, CAMTA1-IT1, PVT1, LINC00491, HULC, MALAT1, C8orf49, KCNQ1OT1, AL139147.1, AL391421.1	Hsa-miR-338	GRIK1-AS1, C5orf64, AC010336.2, LINC00473, FAM95B1, AC110491.1, LINC00402, LINC00484, ADAMTS9-AS2, LINC00461, FRMD6-AS2, PWRN1
Hsa-miR-375	C15orf54, C17orf77, WT1-AS, MUC19, STEAP2-AS1, LMO7-AS1, HOTAIR, OSBPL10-AS1, POU6F2-AS2, MACROD2-AS1, DLEU7-AS1, MALAT1, C8orf49, KCNQ1OT1, AL139147.1	Hsa-miR-17	C20orf166-AS1, C5orf64, AC010336.2, HCG23, JAZF1-AS1, LINC00402, ARHGEF26-AS1
Hsa-miR-183	C20orf166-AS1, AL360004.1, FAM95B1, CHL1-AS2, ADAMTS9-AS2, LINC00507	Hsa-miR-424	C5orf64, AL360004.1, LINC00473, LINC00092, SFTA1P, LINC00484, LINC00461, PWRN1
Hsa-miR-98	LINC00488, FAM95B1, AC110491.1, JAZF1-AS1, LINC00484, ADAMTS9-AS2, PWRN1	Hsa-miR-21	C5orf64, AL360004.1, LINC00488, JAZF1-AS1, ADAMTS9-AS1, ARHGEF26-AS1, PWRN1
Hsa-miR-144	AL360004.1, AC010336.2, LINC00488, ADAMTS9-AS1, ADAMTS9-AS2, LIFR-AS1, LINC00461, PWRN1	Hsa-miR-454	C20orf166-AS1, ADAMTS9-AS1, ADAMTS9-AS2
Hsa-miR-32	JAZF1-AS1, LINC00484, ADAMTS9-AS2, ARHGEF26-AS1	Hsa-miR-141	C5orf64, AC010336.2, FAM95B1, AC110491.1, LINC00402, LINC00484, ADAMTS9-AS2, ARHGEF26-AS1, LINC00461
Hsa-miR-206	LINC00488, FAM95B1, LINC00092, SFTA1P, LINC00163, LINC00484, AL138995.1, LIFR-AS1, FRMD6-AS2	Hsa-miR-372	C20orf166-AS1, AC010336.2, HCG23, JAZF1-AS1, LINC00484, ADAMTS9-AS2, ARHGEF26-AS1, LIFR-AS1, LINC00461

DElncRNAs: Differentially expressed long-noncoding RNAs; DEmiRNAs: Differentially expressed microRNAs.

Table 2 Putative differentially expressed microRNAs that may target differentially expressed mRNAs

DEmiRNAs	DEmRNAs
Hsa-miR-193b	PLAU, PMAIP1, TCF7, CCND1, SHMT2
Hsa-miR-145	SERPINE1, SOX2, MUC1, YES1
Hsa-miR-187	LYN, RNPS1, MYLIP
Hsa-miR-375	TRIM66, USP1, TGFB2, COL12A1, CBX3, SP1
Hsa-miR-150	CBL, ZEB1, HILPDA, SLC7A11, DACH1, EREG, IGF2BP3, KIAA1549, MYB
Hsa-miR-183	KIF5C
Hsa-miR-98	HAND1
Hsa-miR-144	CRIK3
Hsa-miR-182	CHL1, FOXF2, TCEAL7, NPTX1
Hsa-miR-152	NPTX1, BMP3, KLF4
Hsa-miR-454	RBM20, CFL2
Hsa-miR-106a	CFL2, FAM129A, CADM2
Hsa-miR-372	TMEM100, CADM2,
Hsa-miR-17	SLC16A9, CYBRD1, KLF4, CADM2, FAM129A
Hsa-miR-424	TPM2, TMEM100
Hsa-miR-21	ATP2B4, EDIL3, OSR1
Hsa-miR-32	UGP2, PBLD, PHLPP2, ATP2B4
Hsa-miR-141	ELAVL4, EPHA7, PHLPP2
Hsa-miR-338	NOVA1
Hsa-miR-206	SFRP1

Table 3 Top 10 Kyoto Encyclopedia of Genes and Genomes pathways enriched by the differentially expressed mRNAs involved in competing endogenous RNAs networks

Pathway ID	Description	P value	Gene name
hsa05210	Colorectal cancer	8.18E-05	TCF7, CCND1, TGFB2
hsa04115	p53 signaling pathway	1.11E-04	SERPINE1, CCND1
hsa05220	Chronic myeloid leukemia	1.30E-04	CCND1, CBL, TGFB2
hsa05205	Proteoglycans in cancer	1.52E-04	CCND1, CBL, TGFB2, PLAU
hsa05206	MicroRNAs in cancer	6.20E-04	ZEB1, CCND1, PLAU, TGFB2
hsa05216	Thyroid cancer	7.31E-04	TCF7, CCND1
hsa04550	Signaling pathways regulating pluripotency of stem cells	8.67E-04	SOX2, KLF4, HAND1
hsa04310	Wnt signaling pathway	8.84E-04	TCF7, CCND1, SFRP1
hsa05202	Transcriptional misregulation in cancer	1.69E-03	SP1, PLAU, ZEB1
hsa05200	Pathways in cancer	1.74E-03	TCF7, CCND1, CBL, TGFB2