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lncRNA: ENSG00000249859

Summary for PVT1

Gene summary

Gene information	Ensembl ID	ENSG00000249859
	Gene symbol	PVT1
	Gene name	Pvt1 oncogene
	HGNC	9709
	Entrez ID	5820
	Gene type	lincRNA
	Synonyms	PVT1\|08q24.21
	UniProtAcc

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Structure and expression level for PVT1

AS events and RNA A-to-I editing events of lncRNA in TCGA based on Genvode V22 structure.

Differentially expressed gene analysis between cancer and normal samples.

Ensembl ID	Base mean	log2FC(AD/control)	lfcSE	Stat	P-value	Adjc.p-value	DEG direction	Cancer type
ENSG00000249859	3.197475e+02	2.247220e+00	3.261378e-01	6.890401e+00	5.560000e-12	1.420000e-10	UP	GBM
ENSG00000249859	4.262617e+02	3.447230e+00	4.315388e-01	7.988228e+00	1.370000e-15	3.710000e-14	UP	CHOL
ENSG00000249859	8.808086e+02	4.645209e+00	1.208921e-01	3.842443e+01	0.000000e+00	0.000000e+00	UP	KIRC
ENSG00000249859	8.027478e+02	1.294549e+00	2.720399e-01	4.758672e+00	1.950000e-06	1.610000e-05	UP	BLCA
ENSG00000249859	1.602430e+03	2.071891e+00	3.004095e-01	6.896891e+00	5.320000e-12	6.420000e-10	UP	ESCA
ENSG00000249859	6.491228e+02	1.185242e+00	1.192177e-01	9.941825e+00	2.740000e-23	1.070000e-21	UP	PRAD
ENSG00000249859	9.024901e+02	2.432475e+00	1.338030e-01	1.817952e+01	7.500000e-74	3.950000e-72	UP	LUSC
ENSG00000249859	1.159112e+03	1.473736e+00	1.058038e-01	1.392895e+01	4.230000e-44	7.290000e-43	UP	BRCA
ENSG00000249859	6.698446e+02	2.733308e+00	1.487656e-01	1.837326e+01	2.150000e-75	3.570000e-73	UP	LUAD
ENSG00000249859	4.918609e+02	2.817786e+00	1.330257e-01	2.118227e+01	1.390000e-99	1.120000e-96	UP	COAD
ENSG00000249859	9.806756e+02	1.626438e+00	1.812641e-01	8.972755e+00	2.890000e-19	1.770000e-17	UP	STAD
ENSG00000249859	5.445734e+02	2.925517e+00	2.541154e-01	1.151255e+01	1.140000e-30	1.120000e-27	UP	READ

Correlation between lncRNAs and cancer stages.

LncRNA Ensembl ID	Correlation	P-value	Cancer Type	Adjc.p-value
ENSG00000249859	3.140435e-01	5.412731e-03	ACC	1.644374e-02
ENSG00000249859	6.099341e-01	8.673571e-06	CHOL	7.005970e-05
ENSG00000249859	3.122939e-01	2.841810e-12	HNSC	1.706634e-10
ENSG00000249859	4.604988e-01	3.035655e-33	KIRC	2.732090e-31
ENSG00000249859	3.987206e-01	1.935599e-22	PRAD	1.055977e-20

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lncRNA-Protein interaction for PVT1

lncRNA-epigenetic factor interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID	LncRNA ENST ID	LncRNA Name	Protein Ensembl ID	Protein Name	CatRAPID Score	Lncpro Score	UniPortID	Gene Subtype	Public source
ENSG00000249859	ENST00000518528	PVT1	ENSG00000104517	UBR5	37.06	91.0346	O95071	RBP,Epi	NA
ENSG00000249859	ENST00000518528	PVT1	ENSG00000116560	SFPQ	20.7	91.6992	P23246	RBP,Epi	GSE96080,Predict,eCLIP
ENSG00000249859	ENST00000520913	PVT1	ENSG00000116560	SFPQ	18.52	92.7569	P23246	RBP,Epi	GSE96080,Predict,eCLIP
ENSG00000249859	ENST00000523427	PVT1	ENSG00000104517	UBR5	28.08	91.7124	O95071	RBP,Epi	NA
ENSG00000249859	ENST00000519481	PVT1	ENSG00000104517	UBR5	57.04	92.4137	O95071	RBP,Epi	NA
ENSG00000249859	ENST00000517838	PVT1	ENSG00000104517	UBR5	56.41	91.7653	O95071	RBP,Epi	NA
ENSG00000249859	ENST00000504719	PVT1	ENSG00000104517	UBR5	31.85	93.9442	O95071	RBP,Epi	NA
ENSG00000249859	ENST00000504719	PVT1	ENSG00000116560	SFPQ	19.16	90.2938	P23246	RBP,Epi	GSE96080,Predict,eCLIP

lncRNA-transcript factor interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID	LncRNA ENST ID	LncRNA Name	Protein Ensembl ID	Protein Name	CatRAPID Score	Lncpro Score	UniPortID	Gene Subtype	Public source
ENSG00000249859	ENST00000523427	PVT1	ENSG00000167967	E4F1	30.67	92.3412	Q66K89	TF	NA
ENSG00000249859	ENST00000523427	PVT1	ENSG00000147789	ZNF7	17.16	92.156	P17097	TF	NA
ENSG00000249859	ENST00000523427	PVT1	ENSG00000198040	ZNF84	16.43	92.6312	P51523	TF	NA
ENSG00000249859	ENST00000523427	PVT1	ENSG00000196378	ZNF34	11.4	93.3828	Q8IZ26	TF	Predict
ENSG00000249859	ENST00000520913	PVT1	ENSG00000167967	E4F1	41.52	90.0321	Q66K89	TF	NA
ENSG00000249859	ENST00000520913	PVT1	ENSG00000198040	ZNF84	18.51	92.0177	P51523	TF	NA
ENSG00000249859	ENST00000513868	PVT1	ENSG00000102878	HSF4	7.82	91.1043	Q9ULV5	TF	NA
ENSG00000249859	ENST00000518528	PVT1	ENSG00000196378	ZNF34	6.12	90.651	Q8IZ26	TF	Predict
ENSG00000249859	ENST00000520913	PVT1	ENSG00000196378	ZNF34	5.28	90.1563	Q8IZ26	TF	Predict
ENSG00000249859	ENST00000519481	PVT1	ENSG00000167967	E4F1	61.51	90.6971	Q66K89	TF	NA
ENSG00000249859	ENST00000519481	PVT1	ENSG00000198040	ZNF84	33.41	90.1709	P51523	TF	NA
ENSG00000249859	ENST00000504719	PVT1	ENSG00000170631	ZNF16	19.82	91.4334	P17020	TF	NA
ENSG00000249859	ENST00000504719	PVT1	ENSG00000147789	ZNF7	19.61	90.5417	P17097	TF	NA
ENSG00000249859	ENST00000504719	PVT1	ENSG00000198040	ZNF84	18.29	92.377	P51523	TF	NA
ENSG00000249859	ENST00000504719	PVT1	ENSG00000196378	ZNF34	12.3	90.9343	Q8IZ26	TF	Predict

lncRNA-RNA binding protein interaction (#cancer types with positive correlation >= 5).

LncRNA Ensembl ID	LncRNA ENST ID	LncRNA Name	Protein Ensembl ID	Protein Name	CatRAPID Score	Lncpro Score	UniPortID	Gene Subtype	Public source
ENSG00000249859	ENST00000519481	PVT1	ENSG00000178105	DDX10	71.22	90.5791	Q13206	RBP	Predict
ENSG00000249859	ENST00000519481	PVT1	ENSG00000104517	UBR5	57.04	92.1159	O95071	RBP,Epi	NA
ENSG00000249859	ENST00000517838	PVT1	ENSG00000104517	UBR5	56.41	91.6751	O95071	RBP,Epi	NA
ENSG00000249859	ENST00000519481	PVT1	ENSG00000198000	NOL8	51.94	93.8342	Q76FK4	RBP	Predict
ENSG00000249859	ENST00000521600	PVT1	ENSG00000198000	NOL8	42.83	90.5094	Q76FK4	RBP	Predict
ENSG00000249859	ENST00000517525	PVT1	ENSG00000013573	DDX11	42.38	91.0004	Q96FC9	RBP	Predict
ENSG00000249859	ENST00000519481	PVT1	ENSG00000148840	PPRC1	40.89	93.0961	Q5VV67	RBP	Predict
ENSG00000249859	ENST00000504719	PVT1	ENSG00000104517	UBR5	31.85	93.6095	O95071	RBP,Epi	NA
ENSG00000249859	ENST00000504719	PVT1	ENSG00000122965	RBM19	30.08	91.5255	Q9Y4C8	RBP	Predict
ENSG00000249859	ENST00000504719	PVT1	ENSG00000198000	NOL8	28.27	92.6676	Q76FK4	RBP	Predict
ENSG00000249859	ENST00000504719	PVT1	ENSG00000139746	RBM26	26.01	92.531	Q5T8P6	RBP	Predict
ENSG00000249859	ENST00000520913	PVT1	ENSG00000178105	DDX10	67.03	92.8878	Q13206	RBP	Predict
ENSG00000249859	ENST00000513868	PVT1	ENSG00000013573	DDX11	66.81	91.8686	Q96FC9	RBP	Predict
ENSG00000249859	ENST00000513868	PVT1	ENSG00000122965	RBM19	59.82	92.5262	Q9Y4C8	RBP	Predict
ENSG00000249859	ENST00000523068	PVT1	ENSG00000013573	DDX11	55.53	92.0819	Q96FC9	RBP	Predict
ENSG00000249859	ENST00000518528	PVT1	ENSG00000178105	DDX10	52.35	93.4248	Q13206	RBP	Predict
ENSG00000249859	ENST00000520913	PVT1	ENSG00000111641	NOP2	49.94	90.6027	P46087	RBP	NA
ENSG00000249859	ENST00000520913	PVT1	ENSG00000123064	DDX54	48.72	90.4935	Q8TDD1	RBP	GSE89366,PAR-CLIP,Predict
ENSG00000249859	ENST00000522963	PVT1	ENSG00000178105	DDX10	43.4	92.7231	Q13206	RBP	Predict
ENSG00000249859	ENST00000518528	PVT1	ENSG00000013573	DDX11	43.0	90.9046	Q96FC9	RBP	Predict
ENSG00000249859	ENST00000520913	PVT1	ENSG00000198000	NOL8	41.74	94.0197	Q76FK4	RBP	Predict
ENSG00000249859	ENST00000520913	PVT1	ENSG00000162775	RBM15	37.55	90.2961	Q96T37	RBP	ENCODE,eCLIP,iCLIP
ENSG00000249859	ENST00000518528	PVT1	ENSG00000104517	UBR5	37.06	90.5658	O95071	RBP,Epi	NA
ENSG00000249859	ENST00000518528	PVT1	ENSG00000198000	NOL8	36.29	91.9369	Q76FK4	RBP	Predict
ENSG00000249859	ENST00000522963	PVT1	ENSG00000123064	DDX54	33.74	91.1161	Q8TDD1	RBP	GSE89366,PAR-CLIP,Predict
ENSG00000249859	ENST00000517790	PVT1	ENSG00000178105	DDX10	33.48	94.1161	Q13206	RBP	Predict
ENSG00000249859	ENST00000522963	PVT1	ENSG00000198000	NOL8	30.11	92.7921	Q76FK4	RBP	Predict
ENSG00000249859	ENST00000520913	PVT1	ENSG00000148840	PPRC1	27.49	93.3844	Q5VV67	RBP	Predict
ENSG00000249859	ENST00000517790	PVT1	ENSG00000111641	NOP2	26.65	91.431	P46087	RBP	NA
ENSG00000249859	ENST00000517790	PVT1	ENSG00000123064	DDX54	26.02	92.9354	Q8TDD1	RBP	GSE89366,PAR-CLIP,Predict
ENSG00000249859	ENST00000522963	PVT1	ENSG00000148840	PPRC1	22.84	91.9393	Q5VV67	RBP	Predict
ENSG00000249859	ENST00000518528	PVT1	ENSG00000116560	SFPQ	20.7	91.234	P23246	RBP,Epi	GSE96080,Predict,eCLIP
ENSG00000249859	ENST00000520913	PVT1	ENSG00000116560	SFPQ	18.52	92.7871	P23246	RBP,Epi	GSE96080,Predict,eCLIP
ENSG00000249859	ENST00000518528	PVT1	ENSG00000129351	ILF3	17.58	92.9694	Q12906	RBP	ENCODE,eCLIP
ENSG00000249859	ENST00000520913	PVT1	ENSG00000129351	ILF3	16.0	92.6506	Q12906	RBP	ENCODE,eCLIP
ENSG00000249859	ENST00000517790	PVT1	ENSG00000116560	SFPQ	15.21	91.0149	P23246	RBP,Epi	GSE96080,Predict,eCLIP
ENSG00000249859	ENST00000522963	PVT1	ENSG00000129351	ILF3	15.09	90.5912	Q12906	RBP	ENCODE,eCLIP
ENSG00000249859	ENST00000517790	PVT1	ENSG00000129351	ILF3	13.59	94.1169	Q12906	RBP	ENCODE,eCLIP
ENSG00000249859	ENST00000517790	PVT1	ENSG00000111364	DDX55	8.38	90.4645	Q8NHQ9	RBP	ENCODE,Predict,eCLIP
ENSG00000249859	ENST00000522875	PVT1	ENSG00000143621	ILF2	4.08	90.587	Q12905	RBP	NA
ENSG00000249859	ENST00000523190	PVT1	ENSG00000162775	RBM15	47.9	90.7283	Q96T37	RBP	ENCODE,eCLIP,iCLIP
ENSG00000249859	ENST00000615442	PVT1	ENSG00000178105	DDX10	28.6	90.76	Q13206	RBP	Predict
ENSG00000249859	ENST00000523427	PVT1	ENSG00000104517	UBR5	28.08	91.7222	O95071	RBP,Epi	NA
ENSG00000249859	ENST00000523427	PVT1	ENSG00000198000	NOL8	25.89	94.7704	Q76FK4	RBP	Predict
ENSG00000249859	ENST00000523427	PVT1	ENSG00000148840	PPRC1	19.77	92.8737	Q5VV67	RBP	Predict
ENSG00000249859	ENST00000615442	PVT1	ENSG00000129351	ILF3	10.72	92.7544	Q12906	RBP	ENCODE,eCLIP

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lncRNA-DNA interaction for PVT1

lncRNA targets the enhancer region and positively regulates the gene expression.

Only predicted by TDF

DDX11,PUS7,HSF1,CHTOP,RBM19,TFAP4,MYC,ZNF16,SLIRP,NOP2,ILF3,GLI4,TEAD4,RBM39,CENPT,PA2G4,HSF4,THOC6,IRF3,ILF2,JMJD6,ETV4,MRM1,DDX56,PUF60,TIGD5,DDX54,CENPA,LSM4,ATF4,ZNF84,AGO2,CSTF3,TIGD1,RBM26,CPSF1,RNPS1,DDX51,TRA2A,RBM8A,SMYD3,SURF6,DHX34,SRSF2,SRSF7,HINFP,DDX31,CPSF4,RBM15,NR2C1,EIF3B,DDX55,PPIE,SF3B6,SFPQ,UBR5,USF1,ZNF34,THOC1,NOL8,PNPT1

Exist in public source

lncRNA targets the promoter region and positively regulates the gene expression.

Only predicted by TDF

AGO2,E4F1,DDIT3,FOXK2,DDX10,CENPA,UBR5

Exist in public source

lncRNA targets the promoter region and negatively regulates the gene expression.

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lncRNA-RNA interaction for PVT1

lncRNA targets the 3'UTR region and negatively regulates the mRNA.

Only predicted by lncTar

TIGD2,NCOA1

Exist in public source

lncRNA targets the skipped exon region.

-lncRNA and exonskipping events are positively correlated.

LncRNA Ensembl ID

LncRNA ENST ID

Exon ID

Skipped Exon

ndG

Gene name with skipped exon

TransID with skipped exon

ORF mutation

-lncRNA and exonskipping events are negatively correlated.

lncRNA and exonskipping events negative correlated

LncRNA Ensembl ID	LncRNA ENST ID	Exon ID	Skipped Exon	dG	ndG	Gene name with skipped exon	TransID with skipped exon	LOF
ENSG00000249859	ENST00000613916	exon_skip_380242	chr3:186784961-186785101	-11.47	-0.1147	EIF4A2	ENST00000323963	Frame-shift
ENSG00000249859	ENST00000613916	exon_skip_430112	chr4:75653982-75654081	-13.25	-0.1559	G3BP2	ENST00000359707,ENST00000395719	In-frame
ENSG00000249859	ENST00000612011	exon_skip_150854	chr17:32366664-32366757	-8.06	-0.1119	ZNF207	ENST00000321233	In-frame
ENSG00000249859	ENST00000613916	exon_skip_353131	chr20:58669290-58669453	-15.09	-0.1588	STX16	ENST00000371141	Frame-shift
ENSG00000249859	ENST00000613916	exon_skip_446770	chr5:178215275-178215430	-14.79	-0.1155	PHYKPL	ENST00000308158	Frame-shift
ENSG00000249859	ENST00000613916	exon_skip_5818	chr1:45568484-45568684	-13.72	-0.1879	AKR1A1	ENST00000351829,ENST00000372070	Frame-shift
ENSG00000249859	ENST00000613916	exon_skip_11029	chr1:154989559-154989707	-14.08	-0.1805	FLAD1	ENST00000292180	Frame-shift
ENSG00000249859	ENST00000615442	exon_skip_13857	chr1:168038370-168038488	-9.54	-0.1289	DCAF6	ENST00000312263	Frame-shift
ENSG00000249859	ENST00000613916	exon_skip_153096	chr17:44074968-44075087	-12.83	-0.1097	G6PC3	ENST00000269097	Frame-shift

lncRNA targets by miRNA.

LncRNA Ensembl ID

miRNA ID

LncRNA ENST ID

Binding site in lncRNA

Score

Energy

Align Len

Public source

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Variants for PVT1

RNA A-to-I editing events in lncRNA.

LncRNAediting ID	LncRNA Ensembl ID	Chromosome	Editing Position	Strand	Gene Type	Gene Name	Transcript ID	Transcript Type	Transcript Name
LncEditing_207413	ENSG00000249859.6	chr8	127798590	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_207493	ENSG00000249859.6	chr8	127798755	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208403	ENSG00000249859.6	chr8	127808909	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208413	ENSG00000249859.6	chr8	127808910	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208433	ENSG00000249859.6	chr8	127808927	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208443	ENSG00000249859.6	chr8	127808936	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208473	ENSG00000249859.6	chr8	127808944	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208483	ENSG00000249859.6	chr8	127808950	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208493	ENSG00000249859.6	chr8	127808951	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208553	ENSG00000249859.6	chr8	127809013	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208573	ENSG00000249859.6	chr8	127809215	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208623	ENSG00000249859.6	chr8	127809292	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208703	ENSG00000249859.6	chr8	127809379	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208723	ENSG00000249859.6	chr8	127809382	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208743	ENSG00000249859.6	chr8	127809387	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208803	ENSG00000249859.6	chr8	127809456	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208813	ENSG00000249859.6	chr8	127809468	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_208833	ENSG00000249859.6	chr8	127812329	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_209503	ENSG00000249859.6	chr8	127818932	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_209753	ENSG00000249859.6	chr8	127821691	+	lincRNA	PVT1	ENST00000524165.4	lincRNA	PVT1-001
LncEditing_212510	ENSG00000249859.6	chr8	127915469	+	lincRNA	PVT1	ENST00000521951.1	lincRNA	PVT1-002
LncEditing_212546	ENSG00000249859.6	chr8	127915544	+	lincRNA	PVT1	ENST00000521951.1	lincRNA	PVT1-002
LncEditing_213142	ENSG00000249859.6	chr8	127959462	+	lincRNA	PVT1	ENST00000519481.4	lincRNA	PVT1-014
LncEditing_213151	ENSG00000249859.6	chr8	127959486	+	lincRNA	PVT1	ENST00000519481.4	lincRNA	PVT1-014
LncEditing_213154	ENSG00000249859.6	chr8	127959492	+	lincRNA	PVT1	ENST00000519481.4	lincRNA	PVT1-014
LncEditing_213514	ENSG00000249859.6	chr8	127992265	+	lincRNA	PVT1	ENST00000522875.4	lincRNA	PVT1-019
LncEditing_213520	ENSG00000249859.6	chr8	127992266	+	lincRNA	PVT1	ENST00000522875.4	lincRNA	PVT1-019
LncEditing_213720	ENSG00000249859.6	chr8	128003399	+	lincRNA	PVT1	ENST00000522875.4	lincRNA	PVT1-019
LncEditing_213744	ENSG00000249859.6	chr8	128003447	+	lincRNA	PVT1	ENST00000522875.4	lincRNA	PVT1-019
LncEditing_213748	ENSG00000249859.6	chr8	128003463	+	lincRNA	PVT1	ENST00000522875.4	lincRNA	PVT1-019
LncEditing_213764	ENSG00000249859.6	chr8	128003485	+	lincRNA	PVT1	ENST00000522875.4	lincRNA	PVT1-019
LncEditing_213992	ENSG00000249859.6	chr8	128015220	+	lincRNA	PVT1	ENST00000523190.4	lincRNA	PVT1-017
LncEditing_214097	ENSG00000249859.6	chr8	128015564	+	lincRNA	PVT1	ENST00000523190.4	lincRNA	PVT1-017
LncEditing_214137	ENSG00000249859.6	chr8	128015617	+	lincRNA	PVT1	ENST00000523190.4	lincRNA	PVT1-017
LncEditing_214542	ENSG00000249859.6	chr8	128024479	+	lincRNA	PVT1	ENST00000523190.4	lincRNA	PVT1-017

Edited-associated DElncRNAs in cancer.

LncRNA Ensembl ID	LncRNA Index	Cancer Type	Chr_Postion_Strand	AVE1	AVE2	log2FC	W-value	P-value	Adjc.p-value	Change
ENSG00000249859	LncEditing_208703	LAML	chr8_127809379_+	1.337701e+01	6.851244e+00	1.035928e+00	4.395177e+00	1.106826e-05	2.090106e-05	UP
ENSG00000249859	LncEditing_208743	LAML	chr8_127809387_+	1.247763e+01	5.883186e+00	9.219352e-01	6.946289e+00	3.750212e-12	3.456352e-11	UP
ENSG00000249859	LncEditing_208803	LAML	chr8_127809456_+	1.300449e+01	6.510570e+00	1.001850e+00	5.313270e+00	1.076756e-07	3.065900e-07	UP
ENSG00000249859	LncEditing_209503	LAML	chr8_127818932_+	1.366611e+01	6.607846e+00	9.538791e-01	5.066638e+00	4.049030e-07	1.010213e-06	UP
ENSG00000249859	LncEditing_213520	LAML	chr8_127992266_+	1.321531e+01	6.774997e+00	1.037433e+00	4.220793e+00	2.434440e-05	4.264586e-05	UP
ENSG00000249859	LncEditing_213720	LAML	chr8_128003399_+	1.265544e+01	6.056968e+00	9.406543e-01	6.468492e+00	9.898565e-11	5.992514e-10	UP
ENSG00000249859	LncEditing_213748	LAML	chr8_128003463_+	1.230613e+01	6.261798e+00	1.025927e+00	5.664228e+00	1.476878e-08	5.038520e-08	UP
ENSG00000249859	LncEditing_213764	LAML	chr8_128003485_+	1.300257e+01	6.353877e+00	9.679717e-01	5.705766e+00	1.158209e-08	4.098533e-08	UP
ENSG00000249859	LncEditing_214542	LAML	chr8_128024479_+	1.419675e+01	6.642170e+00	9.125471e-01	5.116635e+00	3.110342e-07	7.887624e-07	UP
ENSG00000249859	LncEditing_208493	STAD	chr8_127808951_+	6.166656e+00	2.676315e+00	8.303988e-01	5.566768e+00	2.595081e-08	3.597440e-08	UP
ENSG00000249859	LncEditing_209753	STAD	chr8_127821691_+	5.802933e+00	3.149419e+00	1.134177e+00	4.671464e+00	2.990612e-06	3.666572e-06	UP
ENSG00000249859	LncEditing_212546	STAD	chr8_127915544_+	4.760407e+00	3.136385e+00	1.661179e+00	4.479744e+00	7.473251e-06	8.962894e-06	UP
ENSG00000249859	LncEditing_213154	STAD	chr8_127959492_+	5.547800e+00	3.107680e+00	1.196061e+00	5.326941e+00	9.988032e-08	1.328028e-07	UP
ENSG00000249859	LncEditing_213520	STAD	chr8_127992266_+	5.795235e+00	3.043250e+00	1.076132e+00	6.423557e+00	1.331266e-10	2.198815e-10	UP
ENSG00000249859	LncEditing_213992	STAD	chr8_128015220_+	5.209527e+00	3.160926e+00	1.387338e+00	3.158919e+00	1.583553e-03	1.691012e-03	UP
ENSG00000249859	LncEditing_214097	STAD	chr8_128015564_+	5.288731e+00	3.212539e+00	1.390419e+00	4.027229e+00	5.643805e-05	6.496727e-05	UP
ENSG00000249859	LncEditing_207493	ESCA	chr8_127798755_+	7.580718e+00	3.392833e+00	8.621848e-01	4.676323e+00	2.920652e-06	4.429584e-06	UP
ENSG00000249859	LncEditing_208403	ESCA	chr8_127808909_+	6.768243e+00	3.183890e+00	9.191254e-01	4.280501e+00	1.864728e-05	2.531392e-05	UP
ENSG00000249859	LncEditing_208413	ESCA	chr8_127808910_+	6.649568e+00	3.233859e+00	9.615350e-01	3.939382e+00	8.169189e-05	1.033351e-04	UP
ENSG00000249859	LncEditing_208433	ESCA	chr8_127808927_+	6.574802e+00	3.236052e+00	9.777916e-01	4.023758e+00	5.727668e-05	7.378728e-05	UP
ENSG00000249859	LncEditing_208443	ESCA	chr8_127808936_+	7.406688e+00	3.749229e+00	1.018087e+00	2.679181e+00	7.380253e-03	7.872270e-03	UP
ENSG00000249859	LncEditing_208473	ESCA	chr8_127808944_+	7.183916e+00	3.282644e+00	8.850245e-01	5.332826e+00	9.669574e-08	1.793578e-07	UP
ENSG00000249859	LncEditing_208483	ESCA	chr8_127808950_+	7.808938e+00	3.656357e+00	9.134760e-01	3.491070e+00	4.810910e-04	5.658624e-04	UP
ENSG00000249859	LncEditing_208493	ESCA	chr8_127808951_+	6.051875e+00	3.035745e+00	1.004690e+00	4.276467e+00	1.898827e-05	2.572683e-05	UP
ENSG00000249859	LncEditing_208553	ESCA	chr8_127809013_+	5.183194e+00	4.050073e+00	2.809830e+00	2.600181e+00	9.317472e-03	9.843458e-03	UP
ENSG00000249859	LncEditing_208573	ESCA	chr8_127809215_+	6.791532e+00	3.690863e+00	1.136649e+00	3.143423e+00	1.669845e-03	1.871655e-03	UP
ENSG00000249859	LncEditing_208623	ESCA	chr8_127809292_+	7.836232e+00	3.429941e+00	8.389428e-01	5.113684e+00	3.159351e-07	5.472728e-07	UP
ENSG00000249859	LncEditing_208743	ESCA	chr8_127809387_+	6.444642e+00	2.882714e+00	8.615693e-01	6.154353e+00	7.538442e-10	2.049361e-09	UP
ENSG00000249859	LncEditing_208803	ESCA	chr8_127809456_+	7.041477e+00	3.170707e+00	8.687543e-01	6.209212e+00	5.325082e-10	1.484225e-09	UP
ENSG00000249859	LncEditing_208813	ESCA	chr8_127809468_+	7.324947e+00	3.812255e+00	1.061376e+00	3.762548e+00	1.681908e-04	2.060362e-04	UP
ENSG00000249859	LncEditing_208833	ESCA	chr8_127812329_+	8.110157e+00	3.732491e+00	8.931833e-01	3.032131e+00	2.428340e-03	2.695869e-03	UP
ENSG00000249859	LncEditing_212510	ESCA	chr8_127915469_+	8.250259e+00	3.480386e+00	8.030889e-01	2.628229e+00	8.583075e-03	9.105925e-03	UP
ENSG00000249859	LncEditing_213142	ESCA	chr8_127959462_+	8.576128e+00	3.704645e+00	8.257698e-01	2.654047e+00	7.953267e-03	8.457660e-03	UP
ENSG00000249859	LncEditing_213151	ESCA	chr8_127959486_+	8.027552e+00	3.713297e+00	8.990707e-01	3.263591e+00	1.100100e-03	1.250718e-03	UP
ENSG00000249859	LncEditing_213154	ESCA	chr8_127959492_+	8.097039e+00	3.441210e+00	8.100585e-01	4.301150e+00	1.699136e-05	2.324667e-05	UP
ENSG00000249859	LncEditing_213514	ESCA	chr8_127992265_+	8.078790e+00	3.513166e+00	8.323848e-01	4.480765e+00	7.437592e-06	1.066292e-05	UP
ENSG00000249859	LncEditing_213744	ESCA	chr8_128003447_+	8.167300e+00	3.661886e+00	8.641007e-01	4.290703e+00	1.781081e-05	2.427273e-05	UP
ENSG00000249859	LncEditing_213992	ESCA	chr8_128015220_+	7.611387e+00	3.572828e+00	9.165122e-01	3.669478e+00	2.430466e-04	2.941257e-04	UP
ENSG00000249859	LncEditing_214097	ESCA	chr8_128015564_+	6.890347e+00	3.543495e+00	1.042314e+00	4.281571e+00	1.855788e-05	2.520890e-05	UP
ENSG00000249859	LncEditing_214137	ESCA	chr8_128015617_+	7.707431e+00	3.643919e+00	9.252755e-01	3.111685e+00	1.860230e-03	2.080599e-03	UP

Correlation between RNA A-to-I editing events's frequecy and lncRNA expression.

LncRNA Ensembl ID	LncRNA Index	Correlation	P-value	Adjc.p-value
ENSG00000249859	LncEditing_207413	-4.824370e-01	3.644043e-02	4.081665e-02
ENSG00000249859	LncEditing_208723	-5.032534e-01	2.004099e-02	2.927675e-02
ENSG00000249859	LncEditing_213142	-6.015816e-01	8.263194e-03	1.801401e-02
ENSG00000249859	LncEditing_213744	-6.050992e-01	3.657469e-03	1.137098e-02
ENSG00000249859	LncEditing_213992	4.553034e-01	1.701261e-02	2.653092e-02
ENSG00000249859	LncEditing_208703	-6.877497e-01	3.234302e-03	1.090637e-02
ENSG00000249859	LncEditing_208803	-7.460563e-01	2.846552e-05	8.541607e-04
ENSG00000249859	LncEditing_213720	-4.509021e-01	7.443168e-03	1.686343e-02

Cis-expression quantitative trait loci(cis-eQTL) of lncRNA.

LncRNA Ensembl ID

LncRNA Name

SNP info

Number of Positive corelated Cancer

Positive corelated Cancer

Number of Negative corelated Cancer

Negative corelated Cancer

Top

lncRNAs regulate the target genes through functioning as enhancers

lncRNA regulates differentially expressed genes by function as enhancer.

LncRNA Ensembl ID

PC Gene ID

PC Gene Name

Positive correlated cancers

Cancer with PC gene up-regulation

Cancer with PC gene down-regulation

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lncRNAs regulate the target genes through recruiting transcript factors

LncRNA-TF complex positively regulates the gene expression by target promoter region (#cancer types with positive correlation >= 5).

lncRNA ID	TF ID	TF Name	PCgene ID	PCgene Name	Number of Cancer	Canaer Types
ENSG00000249859	ENSG00000198040	ZNF84	ENSG00000123908	AGO2	6	CHOL,COAD,KIRC,LUAD,PRAD,READ
ENSG00000249859	ENSG00000147789	ZNF7	ENSG00000123908	AGO2	9	ACC,BRCA,CHOL,COAD,KIRC,LUAD,PAAD,PRAD,READ
ENSG00000249859	ENSG00000102878	HSF4	ENSG00000167967	E4F1	5	CHOL,HNSC,KIRC,PAAD,PRAD
ENSG00000249859	ENSG00000147789	ZNF7	ENSG00000167967	E4F1	6	ACC,CHOL,HNSC,KIRC,PAAD,PRAD
ENSG00000249859	ENSG00000147789	ZNF7	ENSG00000104517	UBR5	6	BRCA,CHOL,COAD,LUAD,LUSC,READ

LncRNA-TF complex negatively regulates the gene expression by target promoter region (#cancer types with negative correlation >= 5).

lncRNA ID

TF ID

TF Name

PCgene ID

PCgene Name

Number of Cancer

Canaer Types

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lncRNAs regulate the alternative splicing event through interacting with splicing factor

LncRNA-RBP complex positively regulates the exon skippping events by target skipped eoxon region.

LncRNA Ensembl ID

RBP ID

RBP Gene Name

Exon Skipping ID

Skipped Exon

EX Gene Name

EX Affected TransID

ORF_anno

Cancer Type

LncRNA-RBP complex negatively regulates the exon skippping events by target skipped eoxon region.

LncRNA Ensembl ID

RBP ID

RBP Gene Name

Exon Skipping ID

Skipped Exon

EX Gene Name

EX Affected TransID

ORF_anno

Cancer Type

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lncRNAs regulate mRNA through targeting the 3'-UTR region

lncRNA regulates differential expressed mRNA by directly targeting 3' UTR region.

LncRNA Ensembl ID

LncRNA ENST ID

PC Gene Name

PC Gene ID

PC ENST ID

nDG

Cancer with PC gene up-regulation

Cancer with PC gene Down-regulation

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lncRNAs regulate mRNA by competing with miRNA

lncRNA regulates mRNA by competing the miRNA binding site with mRNA.

LncRNA Ensembl ID

lncRNA-miRNA-mRNA

Cancer Types

Top

lncRNA coding potential

ORFfinder result for the gencode.v22.lncRNA.transcript.fa.

lncRNA Ensembl ID	lncRNA ENST ID	length(AA)	start at transcript	end at transcript
ENSG00000249859.6	ENST00000504719.5	66	88	288
ENSG00000249859.6	ENST00000524165.4	104	312	1
ENSG00000249859.6	ENST00000523328.4	59	8	187
ENSG00000249859.6	ENST00000521951.1	96	288	1
ENSG00000249859.6	ENST00000517525.1	155	1250	783
ENSG00000249859.6	ENST00000523427.1	59	5	184
ENSG00000249859.6	ENST00000517790.1	105	285	602
ENSG00000249859.6	ENST00000522963.4	89	265	534
ENSG00000249859.6	ENST00000518528.1	65	371	565
ENSG00000249859.6	ENST00000523068.1	89	262	531
ENSG00000249859.6	ENST00000521122.1	89	459	728
ENSG00000249859.6	ENST00000513868.5	67	18	218
ENSG00000249859.6	ENST00000520913.1	153	456	917
ENSG00000249859.6	ENST00000519481.4	73	152	373
ENSG00000249859.6	ENST00000517838.4	74	121	345
ENSG00000249859.6	ENST00000512617.5	58	193	17
ENSG00000249859.6	ENST00000521600.4	48	154	8
ENSG00000249859.6	ENST00000522875.4	65	212	406
ENSG00000249859.6	ENST00000523190.4	155	903	436
ENSG00000249859.6	ENST00000522414.1	94	161	442
ENSG00000249859.6	ENST00000616386.1	147	440	0
ENSG00000249859.6	ENST00000617087.1	35	8	112
ENSG00000249859.6	ENST00000613916.1	25	0	77

	lncRNA summary
	lncRNA structure and expression level
	lncRNA-Protein interaction
	lncRNA-DNA interaction
	lncRNA-RNA interaction
	Variants in lncRNA
	lncRNAs regulate the target genes through functioning as enhancers
	lncRNAs regulate the target genes through recruiting transcript factors
	lncRNAs regulate the alternative splicing events through interacting with splicing factor
	lncRNAs regulate mRNA through targeting the 3'-UTR region
	lncRNAs regulate mRNA by competing with miRNA
	lncRNA coding potential